bigdcd file help

From: snoze pa (
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

 I will highly appreciate your help.
Thank you,

ps: Wish you all Happy 4th of July.

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