[gmx-users] simulating several proteins

Cristiano De Michele cristiano.demichele at roma1.infn.it
Wed Mar 10 16:37:14 CET 2010

ok but after I generated two .gro files using genconf (or editconf I  
containing two identical proteins in different positions/orientations
how can I concatenate these two files in order to supply a unique .gro  
file to grompp?

thanks Cristiano

Il giorno 10/mar/10, alle ore 16:27, Mark Abraham ha scritto:

> ----- Original Message -----
> From: Cristiano De Michele <cristiano.demichele at roma1.infn.it>
> Date: Thursday, March 11, 2010 2:25
> Subject: [gmx-users] simulating several proteins
> To: gmx-users at gromacs.org
>> Dear all,
>> is it possible to simulate more than one protein with GROMACS?
>> I would like to simulate two lysozyme proteins not solvated and
>> I tried changing number of proteins in topology file (attached) and
>> then I used this modified .top file to generate a .gro configuration
>> with genbox, but I always end up getting just one protein
>> in the simulation box...
> genbox doesn't take input from the .top file to guide its output.
> Use genconf on your original structure file to multiply it. Then  
> edit your .top by hand to match.
> Mark
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Cristiano De Michele, Ph.D.
Department of Physics                             Tel.  :  +390649913524
University of Rome  "La Sapienza"        Fax  :  +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
homepage: http://pacci.phys.uniroma1.it/
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