Molecule drifts and high average RMSD per residue

From: Ambrish (
Date: Mon Oct 08 2007 - 11:02:49 CDT

I am doing a simulation to test the stability of some modeled structures
(~100 amino acids). The RMSD remains below 1.5 Ang while the values from
rmsd_residue_over_time are ~10 Ang. I looked at the trajectory and found
that the molecule shifts from center towards the edge of the box during the
simulation. I have kept wrapNearest and wrapAll ON and the PME grid sizes
are 64, 64, 54 and am using Langevin piston method.
My questions are:
1. How can I keep my molecule at the center through out the simulation.
2. Are the values from rmsd_residue_over_time high because my molecule
drifts during simulation? Can I bring all the frames in one reference frame
and then calculate rmsd_residue_over_time, to get correct estimate. If yes,
then how do I do that?

I am attaching my configuration file for your concern. Looking forward for
your suggestions.


Ambrish Roy
Graduate Student
Dream is not that what you see in sleep... Dream is the thing which does not
allow you to sleep.
-- Dr. Abdul Kalam

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