[gmx-users] Membrane protein simulation
Mark.Abraham at anu.edu.au
Mon Sep 19 02:12:17 CEST 2011
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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