[gmx-users] Membrane protein simulation

[Mark Abraham]

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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