From: jnsong (
Date: Sun Mar 20 2011 - 22:38:01 CDT

Dear all,

I've tried to use bigdcd.tcl analyses a big NAMD trajectory, but I got
the following results:

1 0.0
2 0.0
3 0.0
4 0.0
5 0.0
6 0.0
7 0.0
8 0.0
9 0.0
10 0.0
11 0.0
12 0.0
13 0.0

rmsd for each frame is 0.0.

In order to check there is no problem with my trajectory file,
I reload the trajectory file to VMD, and type

set all [atomselect top all]
set ref [atomselect top "protein and backbone" frame 0]
set sel [atomselect top "protein and backbone"]
$all move [measure fit $sel $ref]
measure rmsd $sel $ref

and it give the result of '1.1698527336120605'. It proves that nothing
is wrong with my trajectory file.

The TCL script for analysis RMSD is:

set namdpsf ribuamd.psf
set namddcd10 ribua_md_60.dcd

source bigdcd.tcl
set outfile [ open rmsd.dat w ]

proc myrmsd { frame } {
    global mol outfile ref sel all
    $all move [measure fit $sel $ref]
    puts $outfile "$frame [measure rmsd $sel $ref]"

set mol [mol new $namdpsf waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "protein and backbone" frame 0]
set sel [atomselect $mol "protein and backbone"]
bigdcd myrmsd $namddcd10
close $outfile

Could you please give me some help?
Thanks in advance!

Jianing Song
Ph. D. Student 
Institute of Theoretical and Computational Sciences
Dept. Phys.
East China Normal University
3663 North Zhongshan Road
Shanghai, P. R. China