[gmx-users] Drug membrane simulation

Justin Lemkul jalemkul at vt.edu
Fri Oct 27 16:32:18 CEST 2017

On 10/26/17 10:17 PM, Chetan Puri wrote:
> I want to determine permeability of drug molecules through various lipid
> membranes.
> Building the membrane i am able to do with the kalp-dppc tutorial, but for
> placing the drug molecule above the membrane i am not getting proper
> solution.
> So can someone suggest how to place the drug molecule above the membrane
> which contains water also.

You're not going to be successful in trying to force a molecule into a 
box that's already filled with water because atoms will invariably 
overlap and the system won't minimize.  The proper approach is to take a 
membrane, without water, and add the drug to it (either randomly with 
gmx insert-molecules or by specifying its position with gmx editconf and 
appending the coordinates to those of the membrane). Then fill the box 
with water.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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