Re: Molecule drifts and high average RMSD per residue

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 09 2007 - 09:58:06 CDT

The same way one would probably do it by hand: calculate a least-squares
fit of each frame to the reference structure (using vmd's measure fit
command) and move the entire frame accordingly. This is what is done in,
for example, the namd tutorial and the script posted by Prabhu (although
in Prabhu's case, only the selection being compared is actually moved).
Peter

Ilya Chorny wrote:
> How does it align the molecules?
>
> On 10/9/07, *Peter Freddolino* <petefred_at_ks.uiuc.edu
> <mailto: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>
> > <mailto: 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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