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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
