[gmx-users] pressure of NPT simulation after NVT simulation

[Justin Lemkul]

On Mon, Aug 4, 2014 at 9:13 AM, ibrahim khalil <
ibrahim.khalil.chem at gmail.com> wrote:

> Dear gromacs users, I am preparing my system for a production run and I am
> doing the NPT equilibration part. I am facing some problems and I have a
> couple of questions regarding this.
>
> 1. I minimized my system energy to around 3 kJ/mol. Is it sufficiently low?
>
>
No way to know without telling us what the system is and what the goal is.
 The short answer: probably.


> 2. I did the NVT equilibration part and made my system temperature around
> 300K. but whenever i try to do NPT equilibration, the system blows up. Then
> I skipped my NPT equilibration and did my main simulation. When i checked
> the pressure of the system, I found there was a huge initial pressure of
> about 8000 bar. what can i do about it? Should I look for errors in NVT
> equilibration or my NPT equilibration?
>
>
Without a full .mdp file and description of the system, there's no way to
say.


> 3. Should the final pressure of the NVT equilibration match the initial
> pressure of the NPT equilibration?
>
>
Not necessarily.

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
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


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