Hi Sander<br>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)? <br>
<br>Thanks,<br>Sapna<br><br><div class="gmail_quote">On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk <span dir="ltr"><<a href="mailto:pronk@cbr.su.se">pronk@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div style="">It sounds like the normal thing that would happen if you have a system that has no shear elastic constant, like a fluid. <div>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).<div>
<br></div><div>Sander<br><div><br></div><div><br><div><div><div></div><div class="h5"><div>On Mar 30, 2010, at 17:47 , sapna sarupria wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="h5"><div class="gmail_quote">
Hello all,<br><br>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. <br>
<br>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.<br>
<br>Any insights will be helpful. Thanks for the help.<br>
<br>MDP File:<br>title = CO2 hydrate + water ; a string<br>cpp = /lib/cpp ; c-preprocessor<br>dt = 0.002 ; time step<br>nsteps = 25000000 ; number of steps<br>
nstcomm = 10 ; reset c.o.m. motion<br>nstxout = 20000 ; write coords<br>nstvout = 20000 ; write velocities<br>nstlog = 25000 ; print to logfile<br>
nstenergy = 500 ; print energies<br>xtc_grps = OW_HW1_HW2_CO2<br>nstxtcout = 500<br>nstlist = 10 ; update pairlist<br>ns_type = grid ; pairlist method<br>
coulombtype = PME<br>rvdw = 1.2 ; cut-off for vdw<br>rcoulomb = 1.2 ; cut-off for coulomb<br>rlist = 1.2 ; cut-off for coulomb<br>
DispCorr = EnerPres<br>Tcoupl = Nose-Hoover<br>ref_t = 300<br>tc-grps = System<br>tau_t = 0.5<br>Pcoupl = Parrinello-Rahman<br>Pcoupltype = semiisotropic ; pressure geometry<br>
tau_p = 1.0 1.0 ; p-coupling time<br>compressibility = 4.5e-5 4.5e-5 ; compressibility<br>ref_p = 30.5 30.5 ; ref pressure<br>gen_vel = yes ; generate initial vel<br>
gen_temp = 200 ; initial temperature<br>gen_seed = 372340 ; random seed<br>constraint_algorithm = shake<br>constraints = all-bonds<br><br><br><br>Thanks a lot<br>
<font color="#888888">
Sapna<br><br>
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