[gmx-users] NPT simulation stage

[Mahboobeh Eslami]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


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