[gmx-users] position restraint single atom

Justin Lemkul jalemkul at vt.edu
Wed Feb 15 17:00:53 CET 2017

On 2/15/17 9:33 AM, Andrea Spitaleri wrote:
> Hi there,
> I have a dsDNA and I'd like to restraint just two atoms, O3' and O5'
> respectively, in order to mimic the anchor-like to a solid support. I have
> create ad hoc posre.itp file but for some reason the DNA-anchor is moving too
> much from the starting position. I would expect more rigidity around the two
> atoms. Does it sound strange to you? I mean, I was expecting oscillation of the
> whole DNA but keeping the anchors fixed. Are two atoms too little to get this
> kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2.
> Any help/comments on this are welcome.

What about using a larger force constant?  Trying to impede the motion of an 
entire dsDNA using only two atoms as restraints might be difficult to accomplish.



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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