I have changed tau_t=0.2 for 1.0 but the density is not restored. I have tried with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548) , tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion coefficient is indeed half of that with md with sd and tau_t=0.2 (0.71 vs. 1.48 10-5 cm2/s) and about the same with tau_t=1.0 (1.57 10-5 cm2/s). Water is less affected (1009 g/L with md and 1007 g/L with sd and tau_t=0.2). What is the reason why the density is lowered?
Here is the .mdp file (for the simulation with md, tau_t=0.1): title = cyclohexanecpp = /lib/cpp -traditional define = -DFLEXIBLE
constraints = none integrator = sd dt = 0.001 ; fs ! nsteps = 2000000 ; total 2000 ps. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500nstlist = 10 ns_type = grid
rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes energygrps = system ; Berendsen temperature coupling is on in three groups Tcoupl = berendsentau_t = 0.2 tc_grps = System ref_t = 298 ; Pressure coupling is on
Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 11.2e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = no gen_temp = 298.0 gen_seed = 173529 ; Energy group exclusionenergygrp_excl = freezegrps = freezedim = ; Non-equilibrium Thermodynamics acc_grps = accelarate = ; center of mass comm_mode = comm_grps =
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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