VMD-L Mailing List

From: jeela keel (jeela22_at_gmail.com)
Date: Wed Jan 25 2012 - 16:59:19 CST

Hi Alex and John,

yes the frame 0 did not have the required information and starting from
frame1 solved the problem. Thank you for your help

jeela

On Wed, Jan 25, 2012 at 5:03 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
>