[gmx-users] Microwave

[Mostafa Javaheri]

Dear Mark,

The authors didn't circulate the modified version of GROMACS and they
couldn't be able for any help. It would be very kind of you if you could
give me some information about which file or files of the source code
should I alter for achieving this purpose.

Best,

Mostafa

On Mon, Jun 8, 2015 at 8:05 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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