[gmx-users] membrane protein md using gromacs

Itamar Kass ikass at cc.huji.ac.il
Tue Jun 28 10:28:51 CEST 2005

Shalom Rob,
    Try to look at the gromacs site (http://www.gromacs.org/ 
contributions/index.php) look for a file named mdrun_make_hole.tar.gz  
which is used as a modifier of gromacs 3.1.4.  This enable GROMACS to  
make a hole in a membrane based on the inserted protein surface (you  
also need msms).
    The protocol is based on Faraldo-Gomez, J. D., Smith, G. R., and  
Sansom, M. S. (2002). Setting up and optimization of membrane protein  
simulations. European Biophysics Journal 31(3), 217-227.

On Jun 27, 2005, at 7:08 PM, rob yang wrote:

> hi,
> i am trying to simulate glycophorin A dimeric helix in explicit  
> lipid bilayer membrane environment (say, POPC or DMPC). i know that  
> the charmm people have a standard protocol to set up md using  
> CHARMM. i am just wondering if the gromacs community has a standard  
> protocol for such simulations. i've tried to followed the tutorial  
> provided by richard law (http://mccammon.ucsd.edu/~rlaw/ 
> ctbp_workshop_rlaw.htm) but would like to have a more systematic  
> way of setting up the membrane and positioning the helix dimer.
> i also tried the gramicidin A tutorial (http://www.ks.uiuc.edu/ 
> Research/namd/tutorial/NCSA2002/hands-on/) which was very helpful.
> however, the lipid building step did not seem to use a pre- 
> equilibrated lipid library. could anybody give me a pointer to a  
> more elaborated protocol in setting up and running this type of  
> simulation using gromacs? thank you very much in advance.
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| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html

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