[gmx-users] Membrane protein simulation

Sweta Iyer iyer at wehi.EDU.AU
Mon Sep 19 01:42:38 CEST 2011

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.

The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110919/ac154dcd/attachment.html>

More information about the gromacs.org_gmx-users mailing list