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46 lines
2.1 KiB
46 lines
2.1 KiB
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title = NPT equilibration |
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; Run parameters |
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integrator = md ; leap-frog integrator |
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nsteps = 1000 ; 2 * 50000 = 100 ps |
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dt = 0.002 ; 2 fs |
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; Output control |
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nstxout = 500 ; save coordinates every 1.0 ps |
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nstvout = 500 ; save velocities every 1.0 ps |
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nstenergy = 500 ; save energies every 1.0 ps |
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nstlog = 500 ; update log file every 1.0 ps |
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; Bond parameters |
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continuation = yes ; first dynamics run |
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constraint_algorithm = lincs ; holonomic constraints |
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constraints = h-bonds ; bonds involving H are constrained |
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lincs_iter = 1 ; accuracy of LINCS |
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lincs_order = 4 ; also related to accuracy |
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; Neighborsearching |
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cutoff-scheme = Verlet |
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ns_type = grid ; search neighboring grid cells |
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nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme |
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rcoulomb = 0.9613990804113833 ; short-range electrostatic cutoff (in nm) |
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rvdw = 0.9613990804113833 ; short-range van der Waals cutoff (in nm) |
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; Electrostatics |
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coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics |
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pme_order = 4 ; cubic interpolation |
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fourierspacing = 0.16 ; grid spacing for FFT |
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; Temperature coupling is on |
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tcoupl = V-rescale ; modified Berendsen thermostat |
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tc-grps = System ; two coupling groups - more accurate |
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tau_t = 0.1 ; time constant, in ps |
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ref_t = 298.15 ; reference temperature, one for each group, in K |
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; Pressure coupling is on |
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pcoupl = Berendsen ; Pressure coupling on in NPT |
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pcoupltype = isotropic ; uniform scaling of box vectors |
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tau_p = 2.0 ; time constant, in ps |
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ref_p = 1.0 ; reference pressure, in bar |
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compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 |
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refcoord_scaling = com |
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; Periodic boundary conditions |
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pbc = xyz ; 3-D PBC |
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; Dispersion correction |
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DispCorr = EnerPres ; account for cut-off vdW scheme |
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; Velocity generation |
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gen_vel = no ; Velocity generation is off |
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