[gmx-users] Drug membrane simulation

[Justin Lemkul]

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

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

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