VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 25 2012 - 16:03:35 CST

What wrote the DCD file? The DCD file is the source of the PBC info,
so if you're getting zeros, its because either the DCD file contained
no PBC info, or subsequent scripting operations cleared it out.
You might also check that the 0th frame has PBC info, and whether the 1st
and subsequent frames have PBC info, as it may be that just the PDB
file was missing the cell info, but the DCD was okay.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 25, 2012 at 04:56:40PM -0500, jeela keel wrote:
> Dear VMD users,
> I have similar problem that has been discussed before in this thread
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8418.html
> I loaded a pdb file and a trajectory file (dcd) then used the GUI plug-in
> VMD to 'measure gofr' for measuring rdf between protein and water (
> tried selection1 as name of the protein and selection2 as name of the
> water, also tried the resname of protein and resname of water)
> got the following "error measure gofr: unit cell volume is zero". I am
> using the PBC wrap trajectory file.
>
> Similar problem that has been discussed before in this thread
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8418.html but
> did not address how to fix the problem if using the PBC
>
> Any suggestion how to solve the problem of the unit cell or a different
> way of getting the rdf
>
> Thank you for any suggestion and your help
>
> jeela 

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