On 5/30/15 1:25 AM, yoochan wrote:
Dear all,
I’m trying to do umbrella sampling simulation which drugs penetrate the POPC
membrane.
I have trouble what if I do npt or umbrella simulation, the drugs move around
from the initial location.
(I got each 0.1 nm spacing window for npt and umbrella simulation)
Well, the drug should always move, but it should be restrained according to what
settings you're using.
So, these results cannot have suitable G_WHAM analysis because of lack of
results files at the certain coordinates.
Should I have to fix the drugs to keep and satisfy G_WHAM analysis?
Here I linked my simulation results and mdp files.
1.) npt_and_umbrella Simulation results.
https://www.dropbox.com/s/w2gq3y686kmw3uc/npt_vs_umbrella_1.png?dl=0
https://www.dropbox.com/s/w2gq3y686kmw3uc/npt_vs_umbrella_1.png?dl=0
2) npt.mdp
https://www.dropbox.com/s/y1tg4fhxk6mcpul/npt.mdp?dl=0
https://www.dropbox.com/s/y1tg4fhxk6mcpul/npt.mdp?dl=0
3) umbrella.mdp
https://www.dropbox.com/s/0n8bp5rlu6olz3i/umbrella.mdp?dl=0
https://www.dropbox.com/s/0n8bp5rlu6olz3i/umbrella.mdp?dl=0
You're using a restraint in z, which means the drug can move freely in x and y;
this is probably what you're referring to above. The better method for this is
probably the cylinder geometry, which is designed for purposes like these. See
the manual.
-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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