Mercurial > repos > chemteam > gmx_npt
comparison test-data/md.mdp @ 0:69ff679edefd draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
| author | chemteam |
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| date | Thu, 04 Oct 2018 17:38:27 -0400 |
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| -1:000000000000 | 0:69ff679edefd |
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| 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 |