Re: Molecule drifts and high average RMSD per residue

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Tue Oct 09 2007 - 09:53:50 CDT

How does it align the molecules?

On 10/9/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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.
>

-- 
Ilya Chorny Ph.D.

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