[gmx-users] Re: density problems when switching from md to sd integrator
Aymeric Naômé
anaome at fundp.ac.be
Mon Feb 1 16:58:44 CET 2010
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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