[gmx-developers] pbc_dx function

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Oct 10 17:24:25 CEST 2006

Assuming the .gro file format has not changed since your version of gromacs:

1. gromacs3.x/trjconv -f orig.xtc -o orig.gro
2. gromacs3.x/trjconv -f orig.gro -o orig_single.gro -b 0 -e 10.1 (or  
whatever to get a single frame)
3. gromacs1.x/grompp -f orig_single.gro -o new.tpr
4. gromacs1.x/trjconv -f orig.gro -o new.xtc

I have never done this myself, but it should work and require only  
that the .gro format is consistent betewwn version. If the gro format  
differs, you could probably write a script to reformat the orig.gro  

Quoting "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>:

> 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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