It sounds like the normal thing that would happen if you have a system that has no shear elastic constant, like a fluid. In that case, there are no restoring forces against growth of system size in one coordinate with a concomitant decrease in the other coordinates, so eventually this should happen (unless I misunderstand the nature of your system).
Sander On Mar 30, 2010, at 17:47 , sapna sarupria wrote: > 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 > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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