Hi,
This force field was designed to be used with constraints.
First try running with constraints set to all-bonds and without -DFLEXIBLE and
check
the densities again.
Berk
> Date: Mon, 1 Feb 2010 16:58:44 +0100
> From: [email protected]
> To: [email protected]
> Subject: [gmx-users] Re: density problems when switching from md to sd
> integrator
>
> 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 = cyclohexane
> cpp = /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 = 500
> nstlist = 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 = berendsen
> tau_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 exclusion
> energygrp_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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