[gmx-users] PMF trails off to infinity.

Laura Kingsley lkingsle at purdue.edu
Mon Jul 2 22:30:31 CEST 2012

Just for clarification, the PMF is read from right to left and the force 
profile is read from left to right.

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&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

Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
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West Lafayette, IN 47907
Office Phone: (765) 496-6643

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