Re: vmd-l: Re: Molecule drifts and high average RMSD per residue

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 09 2007 - 09:51:07 CDT

Sorry, that first line should ready "RMSDTT should do this"
Peter

Peter Freddolino 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.
>>

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