Fwd: [gmx-users] em and pr

Itamar Kass ikass at cc.huji.ac.il
Fri Jun 18 20:32:46 CEST 2004

   As much as I understand it, at the em.mdp write "integrator          =  
steep" in order to minimize clashes in the the system.  The variable -DPOSRE 
tells the program to use predefined restrains (probably written as 
posre_A.itp ...).  You can write restrain file for the peptide molecule if 
you wish, or constrain the bond length using 'constraints          = 

   BTW Try to equilibrate the system when the peptides are not restrain, after 
all you want them to intereact well with the protein.

  Good Sabbath.

----------  Forwarded Message  ----------

Subject: [gmx-users] em and pr
Date: Friday 18 June 2004 21:04
From: Derrick Guang Yuh Lee <k24dgyl at mun.ca>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

dear gmx-users

i'd like just a confirmation on this, but can i perform an energy
minimization of a system w/ lipids, water, and a peptide, and restrain the
peptide such that it cannot move/will not move, and let everything else
settle around it by simply performing a standard energy minimization, but
changing the define variable in my mdp file to -DPOSRE (which is for my

 - derrick

 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca / derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
                                                              - bruce lee

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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)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html

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