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Hi,<br><br>This force field was designed to be used with constraints.<br>First try running with constraints set to all-bonds and without -DFLEXIBLE and check<br>the densities again.<br><br>Berk<br><br>> Date: Mon, 1 Feb 2010 16:58:44 +0100<br>> From: anaome@fundp.ac.be<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Re: density problems when switching from md to sd integrator<br>> <br>> 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)<br>> , 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)<br>> 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?<br>> <br>> Here is the .mdp file (for the simulation with md, tau_t=0.1):<br>> <br>> title = cyclohexane<br>> cpp = /lib/cpp -traditional <br>> define = -DFLEXIBLE<br>> constraints = none<br>> integrator = sd<br>> dt = 0.001 fs !<br>> nsteps = 2000000 total 2000 ps.<br>> nstcomm = 1<br>> nstxout = 1000<br>> nstvout = 1000<br>> nstfout = 0<br>> nstlog = 500<br>> nstenergy = 500<br>> nstlist = 10 <br>> ns_type = grid<br>> rlist = 1.0<br>> coulombtype = PME<br>> rcoulomb = 1.0<br>> rvdw = 1.4<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 6<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes<br>> energygrps = system<br>> ; Berendsen temperature coupling is on in three groups<br>> Tcoupl = berendsen<br>> tau_t = 0.2 <br>> tc_grps = System <br>> ref_t = 298 <br>> ; Pressure coupling is on<br>> Pcoupl = berendsen<br>> pcoupltype = isotropic<br>> tau_p = 0.5<br>> compressibility = 11.2e-5<br>> ref_p = 1.0<br>> ; Generate velocites is on at 300 K.<br>> gen_vel = no<br>> gen_temp = 298.0<br>> gen_seed = 173529<br>> ; Energy group exclusion<br>> energygrp_excl = <br>> freezegrps = <br>> freezedim = <br>> ; Non-equilibrium Thermodynamics<br>> acc_grps = <br>> accelarate = <br>> ; center of mass<br>> comm_mode = <br>> comm_grps =<br>> <br>> > Dear Aymeric:<br>> ><br>> > 1. Can we please see the entire .mdp files for both simulations? I <br>> > suggest that you use a tau_t=1.0 (0.2 is probably over-damped).<br>> ><br>> > 2. Although any value of tau_t should still produce the correct <br>> > equilibria, your diffusion rates and your overall sampling may be <br>> > slower with sd tau_t=0.2 than they are with md.<br>> ><br>> > 3. Can you reproduce this effect with a box of water?<br>> ><br>> >> -- original message --<br>> >><br>> >> I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,<br>> >> compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).<br>> >> After equilibration and NPT simulation, the system reaches the proper<br>> >> density reported for the model (791g/L). When I switch to a stochastic<br>> >> integrator (with inverse friction coeff. tau_t=0.2 ps) the density<br>> >> rapidly falls to about 765g/L, the potential energy increases, while<br>> >> temperature and pressure fluctuate much more around their specified<br>> >> values. I intend to use this box of cyclohexane for solvation free<br>> >> energy calculations. Can anyone explain what is going on?<br>> >> Thanks in advance<br>> >><br>> >> Aymeric<br>> <br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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