There *should* be no preference, but I seem to remember that one of the artifacts of using Ewald-style electrostatic treatment (such as PME) is that there may be dipole-coupling between periodic images, especially if one symmetry has already been broken. That doesn't mean you shouldn't use PME, though: you're a long way off from the thermodynamic limit, so you can't rely on fluctuations being slow. The situation you're describing will always happen, and with a small number of particles (i.e. less than you can see with the naked eye) it will happen sooner rather than later.
Sander On Mar 30, 2010, at 18:00 , sapna sarupria wrote: > Hi Sander > Thanks for your response. Is there then a preference for z-dimension to > expand (other than the way the system is setup in terms of semi-isotropic > coupling). Would one see an expansion in any one direction if I had the same > system setup with independent pressure coupling for each dimension > (anisotropic)? > > Thanks, > Sapna > > On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk <[email protected]> wrote: > 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
-- 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
