[gmx-users] Membrane protein simulation

[Sweta Iyer]

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.


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