annotate alchemical_run/test-data/Report.txt @ 2:c1bcdba99bb3 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c"

Starting minimization for lambda = 0...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_0.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min0.tpr

Setting the LD random seed to -127141127
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 12987.00
Estimate for the relative computational load of the PME mesh part: 0.21

GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
Command line:
  gmx mdrun -deffnm min0

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file min0.tpr, VERSION 2019.1 (single precision)

Using 1 MPI thread
Using 4 OpenMP threads 


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =           10

Energy minimization reached the maximum number of steps before the forces
reached the requested precision Fmax < 100.

writing lowest energy coordinates.

Steepest Descents did not converge to Fmax < 100 in 11 steps.
Potential Energy  = -8.3125391e+04
Maximum force     =  2.1372287e+04 on atom 1
Norm of force     =  5.1859150e+02

GROMACS reminds you: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." (Watson & Crick)

Starting constant volume equilibration...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_0.mdp -c ../EM/min0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt0.tpr

Setting the LD random seed to -187712966
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Estimate for the relative computational load of the PME mesh part: 0.23

There was 1 note

GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
Command line:
  gmx mdrun -deffnm nvt0

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file nvt0.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 20 to 100, rlist from 1.2 to 1.2


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
50 steps,      0.1 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:        1.458        0.365      399.9
                 (ns/day)    (hour/ns)
Performance:       12.084        1.986

GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck)

Constant volume equilibration complete.
Starting constant pressure equilibration...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_0.mdp -c ../NVT/nvt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt0.cpt -o npt0.tpr

Setting the LD random seed to 2038796930
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory

Last frame         -1 time    0.050   
Using frame at t = 0.05 ps
Starting time for run is 0 ps
Estimate for the relative computational load of the PME mesh part: 0.23

There was 1 note

GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
Command line:
  gmx mdrun -deffnm npt0

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file npt0.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 20 to 100, rlist from 1.2 to 1.2


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
50 steps,      0.1 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:        1.261        0.315      399.9
                 (ns/day)    (hour/ns)
Performance:       13.979        1.717

GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa)

Constant pressure equilibration complete.
Starting production MD simulation...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp -c ../NPT/npt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt0.cpt -o md0.tpr


NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]:
  With PME there is a minor soft core effect present at the cut-off,
  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
  energy conservation, but usually other effects dominate. With a common
  sigma value of 0.34 nm the fraction of the particle-particle potential at
  the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.

Setting the LD random seed to -1773803540
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet

NOTE 2 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory

Last frame         -1 time    0.050   
Using frame at t = 0.05 ps
Starting time for run is 0 ps
Estimate for the relative computational load of the PME mesh part: 0.47

There were 2 notes

GROMACS reminds you: "God is a DJ" (Faithless)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
Command line:
  gmx mdrun -deffnm md0

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file md0.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 10 to 50, rlist from 0.8 to 0.86


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
2000 steps,      2.0 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:       27.033        6.758      400.0
                 (ns/day)    (hour/ns)
Performance:       25.581        0.938

GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart)

Production MD complete.
Ending. Job completed for lambda = 0
Starting minimization for lambda = 1...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_1.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min1.tpr

Setting the LD random seed to -1393309481
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 12987.00
Estimate for the relative computational load of the PME mesh part: 0.21

GROMACS reminds you: "Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia." (Roald Hoffmann)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
Command line:
  gmx mdrun -deffnm min1

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file min1.tpr, VERSION 2019.1 (single precision)

Using 1 MPI thread
Using 4 OpenMP threads 


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =           10

Energy minimization reached the maximum number of steps before the forces
reached the requested precision Fmax < 100.

writing lowest energy coordinates.

Steepest Descents did not converge to Fmax < 100 in 11 steps.
Potential Energy  = -8.3125391e+04
Maximum force     =  2.1372287e+04 on atom 1
Norm of force     =  5.1859150e+02

GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt)

Starting constant volume equilibration...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_1.mdp -c ../EM/min1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt1.tpr

Setting the LD random seed to -1631510067
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Estimate for the relative computational load of the PME mesh part: 0.23

There was 1 note

GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
Command line:
  gmx mdrun -deffnm nvt1

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file nvt1.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 20 to 100, rlist from 1.2 to 1.2


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
50 steps,      0.1 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:        1.273        0.318      399.9
                 (ns/day)    (hour/ns)
Performance:       13.842        1.734

GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter)

Constant volume equilibration complete.
Starting constant pressure equilibration...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_1.mdp -c ../NVT/nvt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt1.cpt -o npt1.tpr

Setting the LD random seed to -166230178
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory

Last frame         -1 time    0.050   
Using frame at t = 0.05 ps
Starting time for run is 0 ps
Estimate for the relative computational load of the PME mesh part: 0.23

There was 1 note

GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
Command line:
  gmx mdrun -deffnm npt1

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file npt1.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 20 to 100, rlist from 1.2 to 1.2


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
50 steps,      0.1 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:        1.310        0.328      399.9
                 (ns/day)    (hour/ns)
Performance:       13.448        1.785

GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses)

Constant pressure equilibration complete.
Starting production MD simulation...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp -c ../NPT/npt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt1.cpt -o md1.tpr


NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]:
  With PME there is a minor soft core effect present at the cut-off,
  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
  energy conservation, but usually other effects dominate. With a common
  sigma value of 0.34 nm the fraction of the particle-particle potential at
  the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.

Setting the LD random seed to -651728442
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet

NOTE 2 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory

Last frame         -1 time    0.050   
Using frame at t = 0.05 ps
Starting time for run is 0 ps
Estimate for the relative computational load of the PME mesh part: 0.47

There were 2 notes

GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
Command line:
  gmx mdrun -deffnm md1

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file md1.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 10 to 50, rlist from 0.8 to 0.86


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
2000 steps,      2.0 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:       27.548        6.887      400.0
                 (ns/day)    (hour/ns)
Performance:       25.103        0.956

GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini)

Production MD complete.
Ending. Job completed for lambda = 1
Starting minimization for lambda = 2...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_2.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min2.tpr

Setting the LD random seed to 886887101
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 12987.00
Estimate for the relative computational load of the PME mesh part: 0.21

GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
Command line:
  gmx mdrun -deffnm min2

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file min2.tpr, VERSION 2019.1 (single precision)

Using 1 MPI thread
Using 4 OpenMP threads 


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =           10

Energy minimization reached the maximum number of steps before the forces
reached the requested precision Fmax < 100.

writing lowest energy coordinates.

Steepest Descents did not converge to Fmax < 100 in 11 steps.
Potential Energy  = -8.3125391e+04
Maximum force     =  2.1372287e+04 on atom 1
Norm of force     =  5.1859150e+02

GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys)

Starting constant volume equilibration...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_2.mdp -c ../EM/min2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt2.tpr

Setting the LD random seed to -902054215
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Estimate for the relative computational load of the PME mesh part: 0.23

There was 1 note

GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
Command line:
  gmx mdrun -deffnm nvt2

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file nvt2.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 20 to 100, rlist from 1.2 to 1.2


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
50 steps,      0.1 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:        1.308        0.327      399.9
                 (ns/day)    (hour/ns)
Performance:       13.471        1.782

GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins)

Constant volume equilibration complete.
Starting constant pressure equilibration...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_2.mdp -c ../NVT/nvt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt2.cpt -o npt2.tpr

Setting the LD random seed to -652502066
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory

Last frame         -1 time    0.050   
Using frame at t = 0.05 ps
Starting time for run is 0 ps
Estimate for the relative computational load of the PME mesh part: 0.23

There was 1 note

GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
Command line:
  gmx mdrun -deffnm npt2

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file npt2.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 20 to 100, rlist from 1.2 to 1.2


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
50 steps,      0.1 ps.

Writing final coordinates.

               Core t (s)   Wall t (s)        (%)
       Time:        1.290        0.323      399.9
                 (ns/day)    (hour/ns)
Performance:       13.659        1.757

GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson)

Constant pressure equilibration complete.
Starting production MD simulation...
                      :-) GROMACS - gmx grompp, 2019.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
Command line:
  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp -c ../NPT/npt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt2.cpt -o md2.tpr


NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]:
  With PME there is a minor soft core effect present at the cut-off,
  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
  energy conservation, but usually other effects dominate. With a common
  sigma value of 0.34 nm the fraction of the particle-particle potential at
  the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.

Setting the LD random seed to 551042888
Generated 45 of the 45 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 45 of the 45 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
Excluding 3 bonded neighbours molecule type 'NA'
Excluding 3 bonded neighbours molecule type 'CL'
Excluding 3 bonded neighbours molecule type 'WAT'
Removing all charge groups because cutoff-scheme=Verlet

NOTE 2 [file morph.top, line 232]:
  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
  an estimated oscillational period of 8.0e-03 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 12987.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory

Last frame         -1 time    0.050   
Using frame at t = 0.05 ps
Starting time for run is 0 ps
Estimate for the relative computational load of the PME mesh part: 0.47

There were 2 notes

GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)

Analysing residue names:
There are:     1      Other residues
There are:    10        Ion residues
There are:  2151      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
This run will generate roughly 1 Mb of data
                      :-) GROMACS - gmx mdrun, 2019.1 (-:

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GROMACS:      gmx mdrun, version 2019.1
Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
Command line:
  gmx mdrun -deffnm md2

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file md2.tpr, VERSION 2019.1 (single precision)
Changing nstlist from 10 to 50, rlist from 0.8 to 0.86


Using 1 MPI thread
Using 4 OpenMP threads 

starting mdrun 'BioSimSpace System'
2000 steps,      2.0 ps.

step 2: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 6 and 15
at distance 47.750 which is larger than the table limit 1.860 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



WARNING: Listed nonbonded interaction between particles 2 and 15
at distance 47.627 which is larger than the table limit 1.860 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


/scratch2/tsenapathi/Projects/BRIDGE/galaxy-tools-compchem/tools/free_energy/alchemical_run/gmx_fep.sh: line 104: 13890 Segmentation fault      gmx mdrun -deffnm md$LAMBDA
Production MD complete.
Ending. Job completed for lambda = 2