[gmx-users] density problems when switching from md to sd integrator

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jan 28 15:50:41 CET 2010

Dear Aymeric:

1. Can we please see the entire .mdp files for both simulations? I  
suggest that you use a tau_t=1.0 (0.2 is probably over-damped).

2. Although any value of tau_t should still produce the correct  
equilibria, your diffusion rates and your overall sampling may be  
slower with sd tau_t=0.2 than they are with md.

3. Can you reproduce this effect with a box of water?

-- original message --

I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
After equilibration and NPT simulation, the system reaches the proper
density reported for the model (791g/L). When I switch to a stochastic
integrator (with inverse friction coeff. tau_t=0.2 ps) the density
rapidly falls to about 765g/L, the potential energy increases, while
temperature and pressure fluctuate much more around their specified
values. I intend to use this box of cyclohexane for solvation free
energy calculations. Can anyone explain what is going on?
Thanks in advance


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