[gmx-users] Should I fix my drugs during membrane penetration simulation?

Justin Lemkul jalemkul at vt.edu
Sat May 30 14:34:06 CEST 2015

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 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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