Re: Molecule drifts and high average RMSD per residue

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 09 2007 - 09:45:23 CDT

RMSD should do this alignment iff you click the align button prior to
calculating RMSDs; it is not automatic.
Peter

Ilya Chorny wrote:
> Does not the RMSD trajectory tool in VMD align the molecules before
> calculating the RMSD. I to am having this drift and the drift looks
> linear.
>
> On 10/8/07, * E. Prabhu Raman* <eraman_at_gmu.edu
> <mailto:eraman_at_gmu.edu>> wrote:
>
> 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
>
> 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
>
>
>
>
> --
> Ilya Chorny Ph.D.

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