[gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

[Justin Lemkul]

On 1/22/16 10:04 AM, anu chandra wrote:
> Dear Gromcas users,
>
> I have been following the Gromcas tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html
> ) for setting up and running MD simulations of membrane proteins. I am
> aiming for a microsecond long simulation. In this regard, I have few
> queries about some of the parameters in mdp file used for production run in
> membrane protein tutorial.
>
> 1. Is it required to use NPT (pressure coupling) rather than NVT for the
> production run if the system is already extensively equilbrated in NPT
> ensemble before taking to the production stage?
>

To some extent, this depends on the force field.  NPT is preferred and most 
modern lipid force fields work best with this ensemble.  With NVT, you wind up 
with a constant lipid area, which can impose surface tension.  This may be bad 
for some force fields.

> 2. The literature suggests to set the random seed generator 'on' for a
> better sampling during simulation. I have noticed that the 'gen_vel = no'
> in the mdp file used for production run in the tutorial. I just wonder,
> will it be safe to set the 'gen_vel=yes' during the production run using
> Gromcas.
>

If you regenerate velocities, what was the point of prior equilibration?

-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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