[gmx-users] Membrane protein simulation
shay.teaching at gmail.com
Mon Sep 19 05:30:56 CEST 2011
Also it is possible that there might be a problem with setting up the
membrane. Have you tried running the membrane without protein?
On Sep 19, 2011 3:32 AM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 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:
> 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.
>> On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>> 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.
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> Michael D. Daily
>> Postdoctoral research associate
>> Pacific Northwest National Lab (PNNL)
>> (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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users