RE: bigdcd file help

From: Cosseddu, Salvatore (
Date: Mon Jul 04 2011 - 04:11:55 CDT

I'm not an expert on bigdcd. But, because you are reading and removing from memory the coordinate file, you are likely losing frame 0 coordinates.

try to load with the psf a pdb file or add something like
animate read dcd solvated_prod-01.dcd beg 0 end 0
after loading psf.

If I said something wrong please forgive me!

Tanti auguri di buona indipendenza

Salvatore Cosseddu
PhD student 
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
-----Original Message-----
From: on behalf of snoze pa
Sent: Mon 04/07/2011 07:29
Subject: namd-l: bigdcd file help
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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