[gmx-developers] pbc_dx function

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 10 09:38:54 CEST 2006

Hi Dallas,

If you want, I could have a look at the script. If I understand it
correctly, in g_sdf you bin your box and assign all atoms to the
proper bin. I have a quick and robust way to do so, without the use of

If you're interested, drop me a line...



On 10/10/06, Dallas B. Warren <Dallas.Warren at vcp.monash.edu.au> wrote:
> Just wondering if someone can provide some insight into this?
> Reason need it, at the time asked first time was hoping to upgrade a
> script g_sdf to work with recent copy of software.  But it wouldn't
> compile since this function had changed.  Wasn't vital, as the script
> would still work.
> Now I have reached the point where I have to get the script upgraded,
> since the files being used are from more recent copies of the software,
> and it gives a fatal error.
> > -----Original Message-----
> > From: gmx-developers-bounces at gromacs.org
> > [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of
> > Dallas B. Warren
> > Sent: Thursday, 18 May 2006 12:38 PM
> > To: Discussion list for GROMACS development
> > Subject: [gmx-developers] pbc_dx function
> >
> >
> > What it the first term passed to this function call?
> >
> > Looking in pbc.h it has "t_pbc *pbc"
> >
> > Have worked out second and third as the points distance is
> > being measured between, and the last is that distance.
> Is it the type of periodic boundary condition?
> Or even better, is there someone that would like to look at the g_sdf
> script to get it working?  It is a bit beyond me, but may be with the
> information above I might be able to fumble my way through it and get it
> going again.
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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