Mercurial > repos > chemteam > gmx_rmsf
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md.mdp Mon Oct 24 22:35:01 2022 +0000 @@ -0,0 +1,50 @@ + + title = OPLS Lysozyme MD simulation + ; Run parameters + integrator = md ; leap-frog integrator + nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns) + dt = 0.002 ; 2 fs + ; Output control + nstxout = 50 ; save coordinates every 10.0 ps + nstvout = 50 ; save velocities every 10.0 ps + nstenergy = 50 ; save energies every 10.0 ps + nstlog = 50 ; update log file every 10.0 ps + nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps + ; nstxout-compressed replaces nstxtcout + compressed-x-grps = System ; group(s) to write to the compressed trajectory file + ; Bond parameters + continuation = yes ; Restarting after NPT + constraint_algorithm = lincs ; holonomic constraints + constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained + lincs_iter = 1 ; accuracy of LINCS + lincs_order = 4 ; also related to accuracy + ; Neighborsearching + cutoff-scheme = Verlet + ns_type = grid ; search neighboring grid cells + nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme + rcoulomb = 1.0 ; Short-range electrostatic cut-off + rlist = 1.0 ; Cut-off distance for the short-range neighbor list. + rvdw = 1.0 ; Short-range Van der Waals cut-off + ; Electrostatics + coulombtype = PME ; method for electrostatics calculations e.g. PME + pme_order = 4 ; cubic interpolation + fourierspacing = 0.16 ; grid spacing for FFT + ; Temperature coupling is on + tcoupl = V-rescale ; modified Berendsen thermostat + tc-grps = Protein Non-Protein ; two coupling groups - more accurate + tau_t = 0.1 0.1 ; time constant, in ps + ref_t = 300 300 ; reference temperature, one for each group, in K + ; Periodic boundary conditions + pbc = xyz ; 3-D PBC + ; Dispersion correction + DispCorr = EnerPres ; account for cut-off vdW scheme + ; Velocity generation + gen_vel = no ; Velocity generation is off + ; Pressure coupling is on + pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT + pcoupltype = isotropic ; uniform scaling of box vectors + tau_p = 2.0 ; time constant, in ps + ref_p = 1.0 ; reference pressure, in bar + compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 + + \ No newline at end of file