VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 25 2012 - 16:03:04 CST

On Wed, Jan 25, 2012 at 4:56 PM, jeela keel <jeela22_at_gmail.com> 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

VMD cannot use data that is not there,
so it is ultimately *your* job to make sure
that all information that is needed, is provided.

if your unit cell volume is zero, that means you
have provided coordinate data without box
information. most likely, your .pdb file has no
box information, and thus you cannot include
it in your analysis. whether you pbc wrapped
the dcd file is irrelevant, since measure gofr
has to apply minimum image conventions
in any case and thus is able to handle unwrapped
trajectories just as well as wrapped ones.

> Any suggestion how to solve the problem of the unit cell or a different way
> of getting the rdf

try using frame 1 (instead of the default of frame 0)
as the first frame, and check if your .pdb and/or
dvd file has box information. you cannot compute
the regular gofr without.

axel.

> Thank you for any suggestion  and your help
>
> jeela 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.