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

[Justin Lemkul]

On 11/30/14 3:27 PM, Hovakim Grabski wrote:
> Dear Gromacs Users,I'm trying to run a simulation between a Dickerson dodecamer(12 basepair DNA) and 6 molecules of Methylene Blue.My  1 question is:
> If I try to  remove COM from DNA, it gives an error, so I have to set comm_grps  = System, but 1) doesn't that affect the Methylene Blue molecules?2) is there any way to  remove COM from DNA without getting an error?
> 2. Or should I just use position restraint on DNA's 5' and 3' ends on one strand?

What purpose is there in introducing such artificiality?

There is no sensible reason to only remove COM motion from part of the system 
during the simulation (and you actually run the risk of the simulation crashing 
due to artifacts for solute-in-water systems).  Only in interfacial systems with 
components having different diffusion coefficients does it really make sense to 
specify separate groups.

-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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