comparison test-data/md.mdp @ 0:f261fded9631 draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
author chemteam
date Mon, 24 Oct 2022 22:35:01 +0000
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2 title = OPLS Lysozyme MD simulation
3 ; Run parameters
4 integrator = md ; leap-frog integrator
5 nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns)
6 dt = 0.002 ; 2 fs
7 ; Output control
8 nstxout = 50 ; save coordinates every 10.0 ps
9 nstvout = 50 ; save velocities every 10.0 ps
10 nstenergy = 50 ; save energies every 10.0 ps
11 nstlog = 50 ; update log file every 10.0 ps
12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
13 ; nstxout-compressed replaces nstxtcout
14 compressed-x-grps = System ; group(s) to write to the compressed trajectory file
15 ; Bond parameters
16 continuation = yes ; Restarting after NPT
17 constraint_algorithm = lincs ; holonomic constraints
18 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
19 lincs_iter = 1 ; accuracy of LINCS
20 lincs_order = 4 ; also related to accuracy
21 ; Neighborsearching
22 cutoff-scheme = Verlet
23 ns_type = grid ; search neighboring grid cells
24 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
25 rcoulomb = 1.0 ; Short-range electrostatic cut-off
26 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
27 rvdw = 1.0 ; Short-range Van der Waals cut-off
28 ; Electrostatics
29 coulombtype = PME ; method for electrostatics calculations e.g. PME
30 pme_order = 4 ; cubic interpolation
31 fourierspacing = 0.16 ; grid spacing for FFT
32 ; Temperature coupling is on
33 tcoupl = V-rescale ; modified Berendsen thermostat
34 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
35 tau_t = 0.1 0.1 ; time constant, in ps
36 ref_t = 300 300 ; reference temperature, one for each group, in K
37 ; Periodic boundary conditions
38 pbc = xyz ; 3-D PBC
39 ; Dispersion correction
40 DispCorr = EnerPres ; account for cut-off vdW scheme
41 ; Velocity generation
42 gen_vel = no ; Velocity generation is off
43 ; Pressure coupling is on
44 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
45 pcoupltype = isotropic ; uniform scaling of box vectors
46 tau_p = 2.0 ; time constant, in ps
47 ref_p = 1.0 ; reference pressure, in bar
48 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
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