[gmx-users] bond

David L. Bostick dbostick at physics.unc.edu
Thu Mar 7 17:08:23 CET 2002

I agree..

This will also make things easier for you as far as monitoring the energy.
You can then use energygroups in the .mdp file for making the interaction
energy show up in the .edr file.  This will make data taking easier for
you, although you will have to go through the pain of merging the two
species into one .itp file.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Thu, 7 Mar 2002, jozef hritz wrote:

> > I would like to bind 2 molecules, a peptide and a 'ligand'.
> > They are both mentioned separately in the same .top file.
> > 
> > Is this possible? I cannot just use the atom numbers, while both molecules
> > start from '1'.
> I think You should have both protein and ligand in the same moleculetype,
> when You would like to create bond between them. Then of course they will
> have different numbering.
> 								Jozef
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