[gmx-users] Restraining two Macromolecules

Justin Lemkul jalemkul at vt.edu
Wed Oct 17 23:55:29 CEST 2012

On 10/17/12 5:46 PM, Arman M. Soufiani 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?!

Restraints can only be applied per [moleculetype] and thus you cannot use an 
index group to merge two separate [moleculetype] entries or attempt to apply 
restraints in this way.

> If yes, I would be happy if you direct me how should I embed it in the .mdp
> file?

You can define any number of statements on one line:

define = -DPOSRES_1 -DPOSRES_2



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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