VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
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
bigdcd_wait
close $outfile
#quit
-------------------------------------------

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
200062
3663 North Zhongshan Road
Shanghai, P. R. China