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

Aymeric Naômé anaome at fundp.ac.be
Thu Jan 28 10:38:41 CET 2010

Dear users,

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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