[gmx-users] Position Restraint or remove COM from DNA
jalemkul at vt.edu
Sun Nov 30 22:08:32 CET 2014
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 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
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