[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Sat Oct 29 11:30:14 CEST 2011

It's appeared new question about G_membed

Does anobody used this algorithm for insertion of their proteins ?
In particular I wounder to know how I can to find optimal parameters (
different scaling factors like in the below command) for insertion in my
system( single alpha helix in DMPC bilayer system) and how I can measure
area per lipid in the output system?

   g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-zinit 1.1 -zend 1.0 -nz 100


2011/10/25 Justin A. Lemkul <jalemkul at vt.edu>

> James Starlight wrote:
>> Justin,
>> I've found the same task of MSU's students :) They simulate membrane
>> formation without NPT stage ( after NVT they run production MD). From they
>> reports I've found that simplest membrane system could be formed within
>> 10-30 Ns.  But what about try to make such simulation in vacuum at first
>> without any water ? Might the bilayer been formed in such conditions?
>> Finally I have small question about pereodic boundaries of such bilayer
>> system.
>> E.g I've done simplest system with water consisted of 8 lipid molecules +
>> some water.
>> This is the representation of the system http://i1209.photobucket.com/**
>> albums/cc394/own11/lipids8.png<http://i1209.photobucket.com/albums/cc394/own11/lipids8.png>
>> I want to simulate bilayer formation as well as concomitant hydrophobic
>> effect ( removing all water from formed bilayer)
>> Does the PBC presented in that example ( 2.64196   2.64196   6.85002 for 8
>> lipids) are enought for such lipid movement? It seems that more free space
>> aree needed for overal turn of lipid molecules. How I can calculate exactly
>>  PBC value required for my system ?
> I agree that your system has insufficient space for any real movement
> without violating the minimum image convention.  Your system must have
> adequate room for any lipid to rotate in any direction, and be of sufficient
> size to accommodate a formed membrane, which will have dimensions dictated
> by the APL for the chosen lipid (and of course, the force field's ability to
> produce that value).
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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