From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Mon Oct 08 2007 - 18:01:18 CDT
I don't think you're MINIMIZING the RMSD (does it make sense to be able to do this, isn't that like cheating?), I think you're computing it for each frame. I believe that there is a plug-in in VMD which aligns each frame to the initial frame of a dynamics run and then computes the RMSD. It's called RMSDTT.
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
----- Original Message ----
From: E. Prabhu Raman <eraman_at_gmu.edu>
To: Ambrish <ambrish.roy_at_gmail.com>
Sent: Monday, October 8, 2007 2:57:00 PM
Subject: Re: namd-l: Molecule drifts and high average RMSD per residue
>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?
Whenever I need to calculate RMSD for each residue,I:
1)Load the trajectory into VMD
2)Run a tcl script which alters the coordinates of each frame so as to
minimize the RMSD of each frame with respect to the first frame of the
trajectory. The script can be found here(pls check it for errors before
3)Write out the altered coordinates onto a file and then compute the
RMSD using my own code.
This procedure ensures that the RMSD of each residue is not due to
drifting of the protein. You might find more info in the VMD forum.
Ph.D Student, Bioinformatics & Computational Biology
George Mason University
-----Inline Attachment Follows-----
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.
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