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

[xiao]

Hi Justin,


Thank you very much for your information


Best regards


Fugui








At 2014-04-22 01:52:09,"Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>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
>
>-- 
>==================================================
>
>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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