On 2/15/17 11:10 AM, Andrea Spitaleri wrote:
How Larger? I used 1000
No idea, but that's the first thing I'd try if using two atoms to resist the
motion of thousands of others.
-Justin
-------- Messaggio originale --------
Oggetto: Re: [gmx-users] position restraint single atom
Da: Justin Lemkul
A: [email protected]
CC:
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
--
==================================================
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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