annotate test-data/npt.mdp @ 1:3a018cc1f690 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:17:57 -0400
parents f425c1453662
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
1 title = OPLS Lysozyme NPT equilibration
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
2 define = -DPOSRES ; position restrain the protein
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
3 ; Run parameters
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
4 integrator = md ; leap-frog integrator
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
5 nsteps = 500 ; 2 * 50000 = 100 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
6 dt = 0.002 ; 2 fs
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
7 ; Output control
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
8 nstxout = 50 ; save coordinates every 1.0 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
9 nstvout = 50 ; save velocities every 1.0 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
10 nstenergy = 50 ; save energies every 1.0 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
11 nstlog = 50 ; update log file every 1.0 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
13 ; Bond parameters
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
14 continuation = yes ; Restarting after NVT
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
15 constraint_algorithm = lincs ; holonomic constraints
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
16 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
17 lincs_iter = 1 ; accuracy of LINCS
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
18 lincs_order = 4 ; also related to accuracy
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
19 ; Neighborsearching
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
20 cutoff-scheme = Verlet
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
21 ns_type = grid ; search neighboring grid cells
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
22 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
23 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
24 rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
25 ; Electrostatics
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
26 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
27 pme_order = 4 ; cubic interpolation
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
28 fourierspacing = 0.16 ; grid spacing for FFT
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
29 ; Temperature coupling is on
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
30 tcoupl = V-rescale ; modified Berendsen thermostat
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
31 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
32 tau_t = 0.1 0.1 ; time constant, in ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
33 ref_t = 300 300 ; reference temperature, one for each group, in K
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
34 ; Pressure coupling is on
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
35 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
36 pcoupltype = isotropic ; uniform scaling of box vectors
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
37 tau_p = 2.0 ; time constant, in ps
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
38 ref_p = 1.0 ; reference pressure, in bar
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
39 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
40 refcoord_scaling = com
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
41 ; Periodic boundary conditions
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
42 pbc = xyz ; 3-D PBC
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
43 ; Dispersion correction
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
44 DispCorr = EnerPres ; account for cut-off vdW scheme
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
45 ; Velocity generation
f425c1453662 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
46 gen_vel = no ; Velocity generation is off