Re: rmsd and simulation

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Fri Nov 05 2004 - 11:23:58 CST

You should not simply compare two configurations --- you should look at
the time series, and make a determination based upon that. There is a
chance that your last configuration will have a very large (or very
small) RMSD compared with the first, which would give you an incorrect
indication of the stability of the trajectory.

Check out the simulaid package:

http://fulcrum.physbio.mssm.edu/~mezei/simulaid/

It is an packaged way to analyze your trajectories.

Cheers,

Mike
On Nov 5, 2004, at 01:24, bora erdemli wrote:

> Dear NAMD users;
>
> I would like to ask you something which gives an idea
> about the simulation that one carried out.
> After the simulation I checked the pairwise rmsd of
> carbon alpha of first and last teajectory, and I would
> like to do a judgement by means of this calculation.
> Can I say that if it is less than let's say 2
> Angstrom, the simulation is ok? In order to do that
> first I take aout the first and last trajectorie's
> coordinates as pdb files, and I use the following
> simple rmsd Tcl code. Does anyone have an ides?
>
> rmsd.tcl
> --------------
> set outfile [open la1st.dat w]
>
> set nf [molinfo top get numframes]
>
> set frame0 [atomselect top "name CA " frame 0]
>
>
> # rmsd calculation loop
>
> for { set i 1 } { $i <= $nf } { incr i } {
>
> set sel [atomselect top "name CA " frame $i]
>
>
> $sel move [measure fit $sel $frame0]
>
> puts $outfile "[measure rmsd $sel $frame0]"
>
>
> }
> close $outfile
>
>
> best regards
>
> =====
> Sabri Bora Erdemli
> Koc University
> Computational Science and Engineering
> Research and Teaching Asistant
> Koc Universitesi pk.218 34550
> sariyer Istanbul/TURKEY
> tel no: 02123381736
> 05326512523
>
>
>
>
>
>
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--
C. Michael McCallum                        
http://chem.cop.uop.edu/cmmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  / 
(209) 946-2607 fax

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