[gmx-users] berendsen vs parrinello-rahman

[Mark Abraham]

Unstable models or unstable initial conditions will behave unpredictably.
Unfortunately you've not given us much to go on.

Mark
On May 16, 2014 6:08 PM, "Nilesh Dhumal" <ndhumal at andrew.cmu.edu> wrote:

> >
> >
> > On 5/16/14, 11:37 AM, Nilesh Dhumal wrote:
> >> Hello,
> >>
> >> I am running the simulation for ionic liquids. I initially did
> >> simulation
> >> with Gromacs VERSION 4.0.7  with "parrinello-rahman" pressure coupling.
> >> Here I pasted temperature and pressure coupling part of mdp file.
> >>
> >> ; Temperature coupling is on
> >> Tcoupl = v-rescale
> >> tau_t = 0.1
> >> tc-grps  =system
> >> ref_t =   350
> >> ; Pressure coupling is  on
> >> Pcoupl              = parrinello-rahman
> >> pcoupltype          = isotropic
> >> tau_p               =  0.5
> >> compressibility     =  4.5e-5
> >> ref_p               =  1.0
> >>
> >> We updated gromacs version to recent  Gromacs VERSION 4.5.5.  With these
> >> parameter during equilibration, I got the error "system is blowing up".
> >> I
> >> changed "parrinello-rahman" pressure coupling to berendsen and able to
> >> run
> >> the simulation.
> >>
> >> ; Temperature coupling is on
> >> ;Tcoupl =  Nose-Hoover
> >> tau_t = 1.0
> >> tc-grps  =system
> >> ref_t = 400.0
> >> ; Pressure coupling is  on
> >> Pcoupl              = berendsen;  parrinello-rahman
> >> pcoupltype          = isotropic
> >> tau_p               =  0.5
> >> compressibility     =  4.5e-5
> >> ref_p               =  1.0
> >>
> >> Is there any changes in recent version in pressure coupling?
> >>
> >
> > Is there any prior equilibration?  Using P-R for the initial phase of
> > equilibration can be unstable.  4.0.7 was a bit more forgiving, and this
> > same
> > issue has been reported several times before with the 4.5.x series, with
> > the
> > solution being to set nstpcouple = 1 for the initial phase of
> > equilibration with
> > P-R.
>
> I did the simulations for two different initial structure.
> 1. Pre-equilibrated 2. New initial structure.
>
> Nilesh
>
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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