On 7/2/12 4:30 PM, Laura Kingsley wrote:
Just for clarification, the PMF is read from right to left and the force profile
is read from left to right.
The dramatic change in the magnitude and sign of the force, coupled with the
steady increase in PMF, indicates to me that some elements of your system are
crashing into one another. In the absence of an accompanying explanation of
what you're doing (description of system, procedure with .mdp parameters, etc)
that's the best I can offer.
-Justin
On 07/02/2012 04:27 PM, Kingsley, Laura J wrote:
Here is a link to both the PMF profile and the force profile:
http://s1064.photobucket.com/albums/u370/laurakingsley/?action=view¤t=pull_fig.jpg
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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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