[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:
>> 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.
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> Michael D. Daily
> Postdoctoral research associate
> Pacific Northwest National Lab (PNNL)
> (formerly Qiang Cui group, University of Wisconsin-Madison)
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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