[gmx-users] Converging the system to 300K and 1bar

[Justin Lemkul]

On 4/28/14, 12:04 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:
> Dear gromacs users,
>
> I am doing a protein-peptide interaction...
> when I do NVT (300K) and NPT (1bar) for 200 ps I get the following results
> using g_energy
>
> Temp.         299.8 K
> Pressure-   -1.7bar
>
> Should I go ahead with MD or should I increase my timings for equilibrating
> the system? And if I have to increase the timing, is there a way to run the
> nvt or npt from previous obtained files?
>

Regarding pressure:

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

For extending simulations:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4

-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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