Hi all, Thanks for your replies,
I searched about the simulation under e/m field and as far as I understood, I have to alter the source code for that, but I don't know how to do this and which part of the source code must change exactly. several studies have been performed by Niall J. English and co ( http://scitation.aip.org/content/aip/journal/jcp/131/3/10.1063/1.3184794) and (http://adsabs.harvard.edu/abs/2003JChPh.118.1589E) which I'm tending to do the same but with different protein, due to the correspondence, they used modified version of GROMACS 3 in their studies. I would be thankful if you could give me some idea about this kind of modification? Best, Mostafa On Tue, Jun 2, 2015 at 4:37 PM, Justin Lemkul <[email protected]> wrote: > > > On 6/2/15 4:31 AM, Mostafa Javaheri wrote: > >> Dear Justin, >> >> How could I simulate a membrane protein while there is microwave >> radiations in >> one direction e.g. in direction of z-axis? Should I change the >> delta-lambda >> > > delta-lambda is a free energy option. > > or Is this accessible via electric field option? If I have to use electric >> field option, should I patch the mdrun ( >> http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun)? >> >> > Electric fields are already supported, but I don't think this is > physically what you want. I have no idea how to microwave an MD simulation. > > -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 > > [email protected] | (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 [email protected]. > -- 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 [email protected].
