[gmx-users] NPT simulation stage

[Mahboobeh Eslami]

dear Mr.alizadeh
thanks for your reply
the repeatability of average pressure is my problem. average pressure isn't  repeatability
when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.
my system is protein-ligand complex. How long do you think is enough for the NPT stage?
Regards
On , Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
 
dear Mr.alizadeh
thanks for your reply
my problem hasn't good repeatability. 
when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.
my system is protein-ligand complex. How long do you think is enough for the NPT stage?
Regards

On Monday, April 28, 2014 12:48 PM, Ali Alizadeh <ali.alizadehmojarad at gmail.com> wrote:
 
Dear Mahboobeh,

I do not know what component your system includes. However, based on my experiences, the fluctuation of pressure is high especially for small and incompressible systems. Besides, you should increase your simulation time. You should not expect that the pressure can converge exactly to the pressure you want. I think(I do not know details of your simulations) pressure fluctuation is natural, of course not for short simulations, the average pressure for equilibriated systems is important.



----------------------dear justin
Thank you for your reply.
My system is about 123,000 atoms and my box is cubic.
I'm following conditions apply:

pcoupl?????????? = Parrinello-Rahman?????
Pcoupltype?????? = Isotropic??????????

tau_p??????????? = 0.5???????????????
compressibility? = 4.5e-5??????????????
ref_p??????????? = 1.0???????????????
refcoord_scaling = com

But the average pressure is not good repeatability.

To fix this problem I did two NPT simulation stageThe first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p? but I did not get any results. Increase the NPT simulation time did not solve the problem.
I strongly need your help
Thank you sincerely for your kindness
On Friday, April 25, 2014 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:




On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote:
> hi GMX users
> please help me
> i want to simulate protein-ligand complex by gromacs4.6.5
> when i repeat NPT simulation stage? many times,? simulation results are very different for the pressure average.I sincerely thank you for your guidance
>

Pressure is probably the most ill-defined quantity in MD simulations.? It can
fluctuate dramatically.? Without the actual numbers, it's hard to comment, but
issues related to pressure have been discussed extensively over the list in the
past and there is useful information in
http://www.gromacs.org/Documentation/Terminology/Pressure.

-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

-- 

Sincerely

Ali Alizadeh