[gmx-users] Distance restraints on two TYR OH groups so that they are together
vytautas1987 at yahoo.com
Thu Mar 16 10:20:46 CET 2017
I altered distance restraints according to your comment into:
[ distance_restraints ]
195 281 1 1 1 0.4 0.44 0.48 1000Still get same issue that 195 and 281 even move away from each other.
Here link to all files again, hopefully it will not be distorted.
How can I drag 195 and 281closer with distance restraints? (not necessary as close as 0.2 nm)
On Wednesday, March 15, 2017 2:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
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
> 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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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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