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.
Chris.
-- 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.
Cheers,
Nick
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://www.gromacs.org/pipermail/gmx-users/attachments/20090402/cab0764b/attachment-0001.html
------------------------------
Message: 6
Date: Thu, 2 Apr 2009 20:07:02 -0700
From: Chih-Ying Lin <[email protected]>
Subject: [gmx-users] PDB structure quality
To: [email protected]
Message-ID:
<5777f3840904022007i
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
