[gmx-users] Microwave

[Alex]

I concur, this is a normal practice. Although I don't really get it,
because GMX has a built-in capability of applying AC electric fields.
Which by the way opens great doors to tinfoil hat research! Will
someone please show that cellphone signal intensity is enough to make
ion channels go nuts? A very necessary field of research, IMO.

Alex


MA> Hi,

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

MA> Mark

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