[gmx-users] Fw: g_membed tool

Dallas Warren Dallas.Warren at monash.edu
Sun Mar 20 22:57:14 CET 2011

Box size is in the last line of the coordinate file, both .gro and .pdb will have the box size / dimensions there.


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mohana lakshmi
Sent: Sunday, 20 March 2011 3:50 AM
To: gromacs users
Subject: [gmx-users] Fw: g_membed tool


Dear all..

I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. 
what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane strucuture file but i don t know how and where to mention the size?
Whether any tutorial is available for transmembrane protein using g_membed tool?

Thank you

Mohanalakshmi N.


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