RE: bigdcd file help

From: Cosseddu, Salvatore (S.M.Cosseddu_at_warwick.ac.uk)
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!

Regards
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
email: S.M.Cosseddu_at_warwick.ac.uk
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of snoze pa
Sent: Mon 04/07/2011 07:29
To: namd-l_at_ks.uiuc.edu
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
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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