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

[Berk Hess]

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: anaome at fundp.ac.be
> To: gmx-users at gromacs.org
> 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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