VMD-L Mailing List
From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Tue Mar 15 2011 - 21:42:10 CDT
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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!
jnsong
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