[gmx-users] NVT and NPT equilibration

[Justin Lemkul]

On 6/9/17 4:53 AM, Pandya, Akash wrote:
> Hi all,
> 
> I want to equilibrate my system and NVT worked fine for me converging onto the 300K set point. However, with the NPT part my average pressure is very low (0.22 bar) compared to the 1 bar set point. Is it necessary to do both equilibration steps in order to progress through to the production MD run? Or will NVT be suffice. I have copied my NPT mdp file to this email.
> 

You have to consider the error bar.

http://www.gromacs.org/Documentation/Terminology/Pressure

0.22 +/- a few hundred is not in any way demonstrably different from the target 
value of 1.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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