[gmx-users] Membrane protein simulation

Michael Daily mdaily.work at gmail.com
Mon Sep 19 02:27:51 CEST 2011

Unfortunately genbox will put waters anywhere there is a space, including
inside the membrane.  This can easily be fixed by making a script to remove
waters that are z +/- ~2 nm from the membrane center (you should run
g_density on the system to figure out the optimal distance filter).  You can
run this after running genbox.

On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 19/09/2011 9:42 AM, Sweta Iyer wrote:
> Hi,
> I embedded my protein of interest into a DMPC membrane by the g_membed tool
> with the following command:
>  g membed -f input.tpr -p system.top  -n index.ndx -xyinit 0.1 -xyend 1.0
> -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
>  I then energy minimized the resultant structure for 1 ns before the
> position restraint dynamics and the productive run.
> My structure looks fine after the em. However, when I do the PR and look at
> the structure it looks weird in that half of the protein is hanging out of
> the membrane and there seems to be a patch of water molecules that seem to
> have entered the membrane.
>  I have no clue what must be possibly going wrong here. Should I have
> equilibrated  the system for longer than 1ns or is it something wrong with
> the membrane insertion.
> Sounds like the advice here might be useful.
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> Mark
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Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
(formerly Qiang Cui group, University of Wisconsin-Madison)
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