[gmx-users] Restraining two Macromolecules

Paulo Netz paulo.netz at gmail.com
Thu Oct 18 00:05:11 CEST 2012

It depends on how the molecules are defined in the topology file.
If the coordinates of both molecules are contained in the main
part of the topology file, only one position restraint file is enough
and it should contain entries for all the non-hydrogen atoms in
both molecules. However, if the coordinates of only
one of the molecules are in the main topology file, whereas the
coordinates for the second molecule are read as .itp file
(include file), or if both are read as include files, then there should
be two position restraint files. If both molecules are built of
building blocks (such as protein, DNA ...) then running separately
pdb2gmx should generate adequate posre files for each of
them. If one of the molecule is not built of standard building
blocks (for instance, if it is a ligand, co-factor...) and
you want nevertheless apply restraints to it in the simulation,
then maybe the better solution is to write a short program
(in C or FORTRAN) or script, which could filter out the
numbering of non-hydrogen atoms.

I hope it can help

Best regards

Paulo Netz
Universidade Federal do Rio Grande do Sul
Porto Alegre, Brazil

On Wed, Oct 17, 2012 at 6:46 PM, Arman M. Soufiani
<armansoufiani at gmail.com>wrote:

> Dear Gromacs users,
> It might seem a simple problem, however, I could not find a correct way to
> define two restrained groups in my .mdp file.
> If I include the following an error appears that notifies me that I am not
> able to define two restraints!
> define = -DPOSRES_1
> define = -DPOSRES_2
> Do I need to make an index for the collection of the atoms of both groups
> and then use one define position restraint for them?!
> If yes, I would be happy if you direct me how should I embed it in the .mdp
> file?
> Regards
> Arman
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