Mercurial > repos > chemteam > gmx_trj
comparison test-data/npt.mdp @ 0:bb0053c4e4f2 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
| author | chemteam |
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| date | Tue, 21 Jan 2020 07:29:43 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:bb0053c4e4f2 |
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| 1 title = OPLS Lysozyme NPT equilibration | |
| 2 define = -DPOSRES ; position restrain the protein | |
| 3 ; Run parameters | |
| 4 integrator = md ; leap-frog integrator | |
| 5 nsteps = 500 ; 2 * 50000 = 100 ps | |
| 6 dt = 0.002 ; 2 fs | |
| 7 ; Output control | |
| 8 nstxout = 50 ; save coordinates every 1.0 ps | |
| 9 nstvout = 50 ; save velocities every 1.0 ps | |
| 10 nstenergy = 50 ; save energies every 1.0 ps | |
| 11 nstlog = 50 ; update log file every 1.0 ps | |
| 12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps | |
| 13 ; Bond parameters | |
| 14 continuation = yes ; Restarting after NVT | |
| 15 constraint_algorithm = lincs ; holonomic constraints | |
| 16 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained | |
| 17 lincs_iter = 1 ; accuracy of LINCS | |
| 18 lincs_order = 4 ; also related to accuracy | |
| 19 ; Neighborsearching | |
| 20 cutoff-scheme = Verlet | |
| 21 ns_type = grid ; search neighboring grid cells | |
| 22 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme | |
| 23 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) | |
| 24 rvdw = 1.0 ; short-range van der Waals cutoff (in nm) | |
| 25 ; Electrostatics | |
| 26 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics | |
| 27 pme_order = 4 ; cubic interpolation | |
| 28 fourierspacing = 0.16 ; grid spacing for FFT | |
| 29 ; Temperature coupling is on | |
| 30 tcoupl = V-rescale ; modified Berendsen thermostat | |
| 31 tc-grps = Protein Non-Protein ; two coupling groups - more accurate | |
| 32 tau_t = 0.1 0.1 ; time constant, in ps | |
| 33 ref_t = 300 300 ; reference temperature, one for each group, in K | |
| 34 ; Pressure coupling is on | |
| 35 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT | |
| 36 pcoupltype = isotropic ; uniform scaling of box vectors | |
| 37 tau_p = 2.0 ; time constant, in ps | |
| 38 ref_p = 1.0 ; reference pressure, in bar | |
| 39 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 | |
| 40 refcoord_scaling = com | |
| 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 |