Hello all, I have a simulation running for a hydrate (with CO2) and water in contact with each other. I run the simulation at 280K at which the hydrate melts and finally the system is just liquid water with CO2 in it. However, as the simulation proceeds the box begins to expand in the z-direction and decreases in the x-y direction considerably. Initially the box has 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates more) and is fine for another 10 ns but after that the dimensions in the x-y direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this point the simulation crashes since my cut-off distance are 1.2 nm.
I am using semi-isotropic pressure coupling but the pressure in the x-y direction and z-direction are the same (=30.5 bar) and so is the compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake is used to maintain their geometry. The simulation time step is 2 fs. Can someone tell me why such a thing happens? I have pasted my mdp file for completeness. I am using Gromacs 4.0.5 and I run the simulations in parallel using 4 processors. Values related to domain decomposition etc are unchanged and the default values are used. Any insights will be helpful. Thanks for the help. MDP File: title = CO2 hydrate + water ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002 ; time step nsteps = 25000000 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 20000 ; write coords nstvout = 20000 ; write velocities nstlog = 25000 ; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 500 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 = 300 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; pressure geometry tau_p = 1.0 1.0 ; p-coupling 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 = 200 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds Thanks a lot Sapna
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