comparison test-data/npt.mdp @ 0:72c2b7992c26 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:14:52 -0500
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-1:000000000000 0:72c2b7992c26
1 title = OPLS Lysozyme NPT equilibration
2 define = -DPOSRES ; position restrain the protein
3 ; Run parameters
4 integrator = md ; leap-frog integrator
5 nsteps = 500 ; 2 * 50000 = 100 ps
6 dt = 0.002 ; 2 fs
7 ; Output control
8 nstxout = 50 ; save coordinates every 1.0 ps
9 nstvout = 50 ; save velocities every 1.0 ps
10 nstenergy = 50 ; save energies every 1.0 ps
11 nstlog = 50 ; update log file every 1.0 ps
12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
13 ; Bond parameters
14 continuation = yes ; Restarting after NVT
15 constraint_algorithm = lincs ; holonomic constraints
16 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
17 lincs_iter = 1 ; accuracy of LINCS
18 lincs_order = 4 ; also related to accuracy
19 ; Neighborsearching
20 cutoff-scheme = Verlet
21 ns_type = grid ; search neighboring grid cells
22 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
23 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
24 rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
25 ; Electrostatics
26 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
27 pme_order = 4 ; cubic interpolation
28 fourierspacing = 0.16 ; grid spacing for FFT
29 ; Temperature coupling is on
30 tcoupl = V-rescale ; modified Berendsen thermostat
31 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
32 tau_t = 0.1 0.1 ; time constant, in ps
33 ref_t = 300 300 ; reference temperature, one for each group, in K
34 ; Pressure coupling is on
35 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
36 pcoupltype = isotropic ; uniform scaling of box vectors
37 tau_p = 2.0 ; time constant, in ps
38 ref_p = 1.0 ; reference pressure, in bar
39 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
40 refcoord_scaling = com
41 ; Periodic boundary conditions
42 pbc = xyz ; 3-D PBC
43 ; Dispersion correction
44 DispCorr = EnerPres ; account for cut-off vdW scheme
45 ; Velocity generation
46 gen_vel = no ; Velocity generation is off