[gmx-users] how many groups shall I use to control the temperature?

[Justin Lemkul]

On 6/12/14, 2:37 AM, 陈功 wrote:
> Dear justin,
>       I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 60000+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups "Protein nonProtein", I found that fluctulation of temperature in group "Protein" are obvious, Im afraid that would have an effect on accuracy on my simulation results. So how many groups shall I use to control the temperature?

What protocol is used in published studies similar to what you're doing?  Small 
groups will have larger fluctuations in temperature, that's a given.  I don't do 
CG simulations, so I don't know how such groups are commonly treated.

-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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