rmsd and simulation

From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Fri Nov 05 2004 - 03:24:59 CST

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?

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

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