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