[gmx-users] how to couple a organic molecule in water

[Justin Lemkul]

On 4/21/14, 7:53 AM, xiao wrote:
> Dear gromacs users,
>
>
> I am doing a simulation of an organic molecule in water solution. The organic molecule has 137 atoms (including hydrogen atoms). I have no idea on how to do temperature coupling. I made two temperature groups, one is water, and the other is the organic molecule. I do not  know whether it is reasonable. Another way is to  couple the organic molecule with the water molecules.  Which way is better?
> Any information on that is appreciated.
>

For a small molecule in water, a single thermostat to the whole system seems to 
be the most sensible approach to me.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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