[gmx-users] intermolecular distance restraints

warren deng warrendnj at gmail.com
Tue Apr 14 11:33:39 CEST 2009

Thank you for the reply, Berk. But I would like to keep the two molecules in
separate moleculetypes, which allows me to use the couple-moltype option for
decouple the interactions between them. In this situation, is there any way
to apply intermolecular distance restraint between atoms on two
moleculetypes? Perhaps using the pull code (umbrella sampling) somehow? Many
thanks for your suggestions,


Berk Hess to me
show details 5:07 PM (20 minutes ago) Reply

fromBerk Hess <gmx3 at hotmail.com>
towarrendnj at gmail.com

dateTue, Apr 14, 2009 at 5:07 PM
subjectRE: intermolecular distance restraint

hide details 5:07 PM (20 minutes ago) Reply


Use pdb2gmx -merge to merge the moleculetypes.
Please send Gromacs questions to the gmx-users list.


Date: Tue, 14 Apr 2009 12:13:10 +0800
Subject: intermolecular distance restraint
From: warrendnj at gmail.com
To: gmx3 at hotmail.com
- Show quoted text -

Hi, Dr. Hess,

In my simulation, I need to restrain distances between atoms on two protein
molecules. But the Gromacs manual on NOE seems to imply that the atom
indices belong to the same molecule type.

So I am wondering whether it is possible to create distance restraint
between two molecule types in Gromacs?

Many thanks,


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