[gmx-users] PMF trails off to infinity.

Kingsley, Laura J Lkingsle at purdue.edu
Mon Jul 2 22:27:58 CEST 2012

Here is a link to both the PMF profile and the force profile: 


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Monday, July 02, 2012 3:56 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PMF trails off to infinity.

On 7/2/12 3:53 PM, Laura Kingsley wrote:
> Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the
> ligand until its COM is very close (a few angstroms) from the dummy atom. Could
> this be causing this behavior? What information would help? I'm having a tough

Collisions between any elements of your system would explain the problem, if it 
looks like what I'm picturing in my head :)

> time getting the figures attached but may be I could email them directly to you?
> Let me know.

Bullet point #4 here provides a suggestion:




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


gmx-users mailing list    gmx-users at gromacs.org
* Only plain text messages are allowed!
* 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

More information about the gromacs.org_gmx-users mailing list