[gmx-users] berendsen vs parrinello-rahman

[Nilesh Dhumal]

>
>
> 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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