From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Jul 04 2011 - 01:29:23 CDT
Dear NamD users,
I am trying to calculate rmsd from my dcd files. the namd rmsd tcl script is
working fine. Unfortunately, My system size is big and I have multiple dcd
file for 1ns each.
I am trying big dcd file to get rmsd but somehow it is not working. Here is
my script
proc myrmsd { frame } {
global ref sel all
$all move [measure fit $sel $ref]
puts "$frame: [measure rmsd $sel $ref]"
}
set mol [mol new solvated.psf type psf waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
bigdcd myrmsd dcd solvated_prod-01.dcd solvated_prod-02.dcd
solvated_prod-03.dcd
bigdcd_wait
quit
I will highly appreciate your help.
Thank you,
S
ps: Wish you all Happy 4th of July.
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