On 11/12/14 8:08 AM, liuyong_1...@dicp.ac.cn wrote:
Dear Gromacs users!
I use the flat-bottomed position restraints to avoid the molecules to escape
from the clusters to the vacuum. The parameters of the restraints on water
molecules are shown as follow:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct g r(nm) k
1 2 1 3 30.0
2 2 1 3 30.0
3 2 1 3 30.0
#endif
However, water molecules still escape away from the cluster to the vacuum after
about 100 ns MD run at 550K. What should be done with the restraints to avoid
the water molecules to escape to the vacuum?
Are you using suitable reference coordinates passed to grompp -r? If you're
not, then the reference coordinates are whatever is in grompp -c, which means
your water molecules can deviate up to 3 nm from that position without penalty.
For a sphere, the reference coordinates for the water should be the geometric
center of the sphere.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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