comparison test-data/md.mdp @ 0:7b23265126b0 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:12:39 -0500
parents
children bfb65cb551d8
comparison
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-1:000000000000 0:7b23265126b0
1 title = OPLS Lysozyme MD simulation
2 ; Run parameters
3 integrator = md ; leap-frog integrator
4 nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns)
5 dt = 0.002 ; 2 fs
6 ; Output control
7 nstxout = 50 ; save coordinates every 10.0 ps
8 nstvout = 50 ; save velocities every 10.0 ps
9 nstenergy = 50 ; save energies every 10.0 ps
10 nstlog = 50 ; update log file every 10.0 ps
11 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
12 ; nstxout-compressed replaces nstxtcout
13 compressed-x-grps = System ; replaces xtc-grps
14 ; Bond parameters
15 continuation = yes ; Restarting after NPT
16 constraint_algorithm = lincs ; holonomic constraints
17 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
18 lincs_iter = 1 ; accuracy of LINCS
19 lincs_order = 4 ; also related to accuracy
20 ; Neighborsearching
21 cutoff-scheme = Verlet
22 ns_type = grid ; search neighboring grid cells
23 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
24 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
25 rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
26 ; Electrostatics
27 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
28 pme_order = 4 ; cubic interpolation
29 fourierspacing = 0.16 ; grid spacing for FFT
30 ; Temperature coupling is on
31 tcoupl = V-rescale ; modified Berendsen thermostat
32 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
33 tau_t = 0.1 0.1 ; time constant, in ps
34 ref_t = 300 300 ; reference temperature, one for each group, in K
35 ; Pressure coupling is on
36 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
37 pcoupltype = isotropic ; uniform scaling of box vectors
38 tau_p = 2.0 ; time constant, in ps
39 ref_p = 1.0 ; reference pressure, in bar
40 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
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