On 3/15/17 6:28 AM, Vytautas Rakeviius wrote:
Hello, I try to add distance restraints on two TYR OH groups so that they are
together in the end like this:
[ distance_restraints ]
195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further
away from each other.
Here I share my all files:MD_4AK0_test_pub.tar.bz2
That's not a valid link.
If you're trying to keep 2 oxygen atoms at a distance of 0.2 nm, that's well
within the (likely) repulsive wall of the LJ potential, as well as being
repulsive from the perspective of the electrostatics. You'll either need a
massive biasing force to keep them close, or develop a different way to keep
them at such a distance. Why are you imposing this bias, and at such a short
distance?
-Justin
System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong
way?
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MD_4AK0_test_pub.tar.bz2
MediaFire is a simple to use free service that lets you put all your photos,
documents, music, and video in a si... | |
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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