Mercurial > repos > chemteam > gmx_rmsf
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 |
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| date | Mon, 24 Oct 2022 22:35:01 +0000 |
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| -1:000000000000 | 0:f261fded9631 |
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| 1 | |
| 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 | |
| 49 | |
| 50 |