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
Aymeric
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