Re: Molecule drifts and high average RMSD per residue

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 Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 rwoodphd_at_yahoo.com ----- Original Message ---- From: E. Prabhu Raman <eraman_at_gmu.edu> To: Ambrish <ambrish.roy_at_gmail.com> Cc: namd-l_at_ks.uiuc.edu Sent: Monday, October 8, 2007 2:57:00 PM Subject: Re: namd-l: Molecule drifts and high average RMSD per residue Ambrish: >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 using it): http://binf.gmu.edu/eraman/downloads/adjusted_rmsd.tcl 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. -Prabhu E.Prabhu Raman Ph.D Student, Bioinformatics & Computational Biology George Mason University -----Inline Attachment Follows----- 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 ____________________________________________________________________________________ Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/

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