Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated.
MDP File title = 100% occupancy CO2 hydrate ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002 ; time step nsteps = 15000000 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 0000 ; write coords nstvout = 0000 ; write velocities nstlog = 25000 ; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw = 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist = 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 270 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; pressure geometry tau_p = 1.0 1.0 ; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp = 260 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds ------- Thank you, Sincerely, Sapna
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