Dear Gmx Users, Could you please assess my mdp file on GPUs:
title = Protein-ligand complex MD simualation ; Run parameters integrator = md ; leap-frog integrator nsteps = 100000000 ; 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output ; output coordinates every 25 ps nstvout = 0 ; velocities to output every 25000 steps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 10000 ; suppress (tlumic) xtc trajectory continuation = yes ; first dynamics run 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 verlet-buffer-drift = 0.005 ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs vdwtype = cut-off rvdw-switch = 1.0 rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) vdw-modifier = Potential-shift ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential rcoulomb ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT coulomb-modifier = Potential-shift ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = System ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; pressure coupling is on for 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution nstcalclr = 1 ;period between calculations of long-range every step Let me know if you see something wrong please. It seems it works well. Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
