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:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox
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.
-Justin
On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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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--
====================================
Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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