Re: Molecule drifts and high average RMSD per residue

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Mon Oct 08 2007 - 16:17:33 CDT

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> 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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