VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Tue Sep 25 2012 - 11:43:52 CDT

Not tested

Open a file
Set fh1 [open "rmsd.plt" w]
Make it global and in the proc add

puts $fh1 "$frame: [measure rmsd $sel $ref]"

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of flavio seixas
Sent: Tuesday, September 25, 2012 8:16 AM
To: VMD List
Subject: vmd-l: Big DCD file help

Hi,

I am trying to calculate rmsd from my dcd files. The namd rmsd tcl script is working fine. Unfortunately the values appears listed in tk window and can not be copied at all.
Is possible to put the rmsd values in a file?

This 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 addfile CALDHmT178_wb_min4.pdb type pdb waitfor all] set all [atomselect $mol all] set ref [atomselect $mol "name CA" frame 0] set sel [atomselect $mol "name CA"] bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd bigdcd_wait