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