[gmx-users] berendsen vs parrinello-rahman

[Michael Shirts]

Berendsen has the right average volume, but not the right distribution of
volumes.

http://pubs.acs.org/doi/abs/10.1021/ct300688p

Did you equilibrate berendsen until the volume stabilized and THEN switch
to parrinello-rahman for production?  That's the suggested thing to do.


On Fri, May 16, 2014 at 5:25 PM, Nilesh Dhumal <ndhumal at andrew.cmu.edu>wrote:

> One initial structure is  equilibrated for 10ns  using Gromacs VERSION
> 4.0.7. If I run same structure with same .mdp and same force field
> parameters   using gromacs VERSION 4.5.5. I got the error system is
> blowing up.
> I made another new initial structure which is not equilibrated and I got
> the same error. After changing pressure coupling from parrinello-rahman to
> berendsen , both the simulations went well.
>
> Nilesh
>
>
> > 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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