[gmx-users] PMF calculation using pull code (constraint force method): constrained atom seems to be moving

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Apr 3 05:25:09 CEST 2009

1: Did you "constrain" or "restrain" the distance? Providing your .mdp  
file would help us to figure this out. The terms are quite different  
on this list.

2: The atom "danced around the expected position" ... are you sure  
that it "danced" around x and z, not just Y?

3: If your distance is longer than 1/2 your box length, then the atom  
used to determine your "box" is important. Is this the case? If so,  
probably this is your problem.

Overall: Your expectation is correct, but it is unclear if your  
implementation is correct. Please provide more information.


-- original message ---

I am performing a PMF calculation using the pull code. I selected one fixed
atom as a reference group and constrained another atom with respect to this
reference group so that their separation in the x- and z-directions remain
constant. After running the simulation, I visualized the trajectory and
found that the constrained atom dances around the expected position (it did
not drift away though).

Is this expected at all? I had thought that when I constrained the atom with
respect to the reference group, its position should remain precisely as
defined by the constraints.

I am using the NVT ensemble.


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Message: 6
Date: Thu, 2 Apr 2009 20:07:02 -0700
From: Chih-Ying Lin <chihying2008 at gmail.com>
Subject: [gmx-users] PDB structure quality
To: gmx-users at gromacs.org

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