[gmx-users] Отв: Position Restraint or remove COM from DNA

[Justin Lemkul]

On 12/1/14 4:13 PM, Hovakim Grabski wrote:
> I'm trying to find the binding sites of 6 Methylene Blue molecules on DNA.
> If I remove COM from the whole system, it also affects the Methylene Blue
> molecules, isn't it right?
>

You're not removing the motion of the molecules; you're removing artificial 
drift of the system, e.g. net COM motion, that may accumulate.  For solutes in 
water, the only sensible choice is comm-grps = System.

-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 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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