[gmx-users] Microwave

[Mostafa Javaheri]

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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