[gmx-users] Membrane protein simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 19 02:31:13 CEST 2011

Michael Daily wrote:
> 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.

An even simpler approach is outlined here:


It seems to me that the original problem either derives from incorrect 
construction, incorrect application of position restraints, or as Mark 
suggested, an artifact of PBC.


> On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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)
> 509-375-4581
> (formerly Qiang Cui group, University of Wisconsin-Madison)


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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