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

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

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

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