[gmx-users] Energy of part of system

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Wed Jun 21 17:01:10 CEST 2006

Then you shall make them as a group before the simulation...

Fortunately, there is -rerun for mdrun.
I suggest the following way:
1. Use make_ndx to make groups for three DNA molecules respectively, namely d1, d2 and d3. The 4th groups is of course sol.
2. Set unconstained_start=no in the mdp file.
3. Set energygrps=d1 d2 d3 sol in the mpd file.
4. Use mdrun -rerun your.xtc

Yang Ye

----- Original Message ----
From: Beniamino Sciacca <superbenji83 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, June 21, 2006 10:26:05 PM
Subject: [gmx-users] Energy of part of system

Dear gmx user,
my system is: three DNA molecules solvated in water and ions.
At the end of md I would to know the interaction energy between the 
three molecules of DNA.
How can I do?
If I use g_energy and I choose "Potential" I obtain the potential energy 
of the whole system, isn't it?
But I want the interaction energy.....

Thanks in advance
Beniamino Sciacca

gmx-users mailing list    gmx-users at gromacs.org
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060621/825f2197/attachment.html>

More information about the gromacs.org_gmx-users mailing list