[gmx-users] PMF trails off to infinity.

[Justin A. Lemkul]

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&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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