[gmx-users] berendsen vs parrinello-rahman

Nilesh Dhumal ndhumal at andrew.cmu.edu
Fri May 16 23:25:58 CEST 2014


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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