[gmx-users] Membrane protein simulation

[Shay Teaching]

Also it is possible that there might be a problem with setting up the
membrane. Have you tried running the membrane without protein?
-Shay
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:
>
>
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.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at 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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