[gmx-users] em and pr

Itamar Kass ikass at cc.huji.ac.il
Fri Jun 18 20:24:25 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.

On Friday 18 June 2004 21:04, Derrick Guang Yuh Lee wrote:
> 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
> peptide)?
>  - 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
> catalyst."
>                                                               - 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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