Molecule drifts and high average RMSD per residue

From: Ambrish (ambrish.roy_at_gmail.com)
Date: Mon Oct 08 2007 - 11:02:49 CDT

Hi,
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.

Best,

-- 
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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