[gmx-users] all-bonds

Enemark Soeren chees at nus.edu.sg
Thu Sep 24 05:18:44 CEST 2009

 Thank you so much for your input, Mark!

 For some reason I was so focused on turning the constraints off for a
group that I couldn't see that I can just imitate the way grompp works
and turn on the constraints for the rest of the system. Aiaaah!


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Wednesday, September 23, 2009 3:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] all-bonds

Enemark Soeren wrote:
> Dear GMX-users,
> Is it possible to exclude a group of atoms or molecules from having 
> their bonds converted to constraints when using the all-bonds

Not automatically, but you can edit the topology manually to specify [ 
constraints ] instead of [ bonds ] for those bonds you wish to be 
constraints. See chapter 5 for detail.

gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list