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comparison test-data/md.mdp @ 9:a97dcfc23b4b draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:00:42 -0400
parents 1a5960636405
children
comparison
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8:4b4232c98b6e 9:a97dcfc23b4b
1 title = OPLS Lysozyme MD simulation 1
2 ; Run parameters 2 title = OPLS Lysozyme MD simulation
3 integrator = md ; leap-frog integrator 3 ; Run parameters
4 nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns) 4 integrator = md ; leap-frog integrator
5 dt = 0.002 ; 2 fs 5 nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns)
6 ; Output control 6 dt = 0.002 ; 2 fs
7 nstxout = 50 ; save coordinates every 10.0 ps 7 ; Output control
8 nstvout = 50 ; save velocities every 10.0 ps 8 nstxout = 50 ; save coordinates every 10.0 ps
9 nstenergy = 50 ; save energies every 10.0 ps 9 nstvout = 50 ; save velocities every 10.0 ps
10 nstlog = 50 ; update log file every 10.0 ps 10 nstenergy = 50 ; save energies every 10.0 ps
11 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps 11 nstlog = 50 ; update log file every 10.0 ps
12 ; nstxout-compressed replaces nstxtcout 12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
13 compressed-x-grps = System ; replaces xtc-grps 13 ; nstxout-compressed replaces nstxtcout
14 ; Bond parameters 14 compressed-x-grps = System ; group(s) to write to the compressed trajectory file
15 continuation = yes ; Restarting after NPT 15 ; Bond parameters
16 constraint_algorithm = lincs ; holonomic constraints 16 continuation = yes ; Restarting after NPT
17 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained 17 constraint_algorithm = lincs ; holonomic constraints
18 lincs_iter = 1 ; accuracy of LINCS 18 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
19 lincs_order = 4 ; also related to accuracy 19 lincs_iter = 1 ; accuracy of LINCS
20 ; Neighborsearching 20 lincs_order = 4 ; also related to accuracy
21 cutoff-scheme = Verlet 21 ; Neighborsearching
22 ns_type = grid ; search neighboring grid cells 22 cutoff-scheme = Verlet
23 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme 23 ns_type = grid ; search neighboring grid cells
24 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) 24 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
25 rvdw = 1.0 ; short-range van der Waals cutoff (in nm) 25 rcoulomb = 1.0 ; Short-range electrostatic cut-off
26 ; Electrostatics 26 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
27 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics 27 rvdw = 1.0 ; Short-range Van der Waals cut-off
28 pme_order = 4 ; cubic interpolation 28 ; Electrostatics
29 fourierspacing = 0.16 ; grid spacing for FFT 29 coulombtype = PME ; method for electrostatics calculations e.g. PME
30 ; Temperature coupling is on 30 pme_order = 4 ; cubic interpolation
31 tcoupl = V-rescale ; modified Berendsen thermostat 31 fourierspacing = 0.16 ; grid spacing for FFT
32 tc-grps = Protein Non-Protein ; two coupling groups - more accurate 32 ; Temperature coupling is on
33 tau_t = 0.1 0.1 ; time constant, in ps 33 tcoupl = V-rescale ; modified Berendsen thermostat
34 ref_t = 300 300 ; reference temperature, one for each group, in K 34 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
35 ; Pressure coupling is on 35 tau_t = 0.1 0.1 ; time constant, in ps
36 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT 36 ref_t = 300 300 ; reference temperature, one for each group, in K
37 pcoupltype = isotropic ; uniform scaling of box vectors 37 ; Periodic boundary conditions
38 tau_p = 2.0 ; time constant, in ps 38 pbc = xyz ; 3-D PBC
39 ref_p = 1.0 ; reference pressure, in bar 39 ; Dispersion correction
40 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 40 DispCorr = EnerPres ; account for cut-off vdW scheme
41 ; Periodic boundary conditions 41 ; Velocity generation
42 pbc = xyz ; 3-D PBC 42 gen_vel = no ; Velocity generation is off
43 ; Dispersion correction 43 ; Pressure coupling is on
44 DispCorr = EnerPres ; account for cut-off vdW scheme 44 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
45 ; Velocity generation 45 pcoupltype = isotropic ; uniform scaling of box vectors
46 gen_vel = no ; Velocity generation is off 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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