[gmx-users] PMF trails off to infinity.

[Kingsley, Laura J]

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

http://s1064.photobucket.com/albums/u370/laurakingsley/?action=view&current=pull_fig.jpg


-----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:

http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


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