[gmx-users] Spherical Position Restrain from the center of the Box

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 30 18:11:02 CET 2011

Hi Ricardo,

Unfortunately that is not possible. What you can do is rearrange the water
in the structure and use two water moleculetypes, one with and one without
position restraints. It might be nice to have something like
global_position_restraints, added under [ system ], but that needs to be
implemented first.



On Nov 30, 2011 6:03 PM, "Ricardo O. S. Soares" <ross_usp at yahoo.com.br>

Hello dear GMX Users,

Through scripting, I have an itp-like file to restrain all atoms that are
NOT within a 30 angstroms radius from the center (a trimmer + water + ions).
This selection includes both protein and solvent atoms, which may be a
problem when assigning this selection to the TOP file.
Is there a way to include this whole selection into the top file directly?
Where/how could that be?
I've searched for solutions for a while, with no avail.




Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São

gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111130/7ae08c32/attachment.html>

More information about the gromacs.org_gmx-users mailing list