[gmx-users] Microwave

[Mark Abraham]

Hi,

You'd have to contact the authors to get their modified version.

Mark

On Sun, Jun 7, 2015 at 11:09 PM Mostafa Javaheri <javaheri.gromacs at gmail.com>
wrote:

> 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 <jalemkul at vt.edu> 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
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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