[gmx-users] Reading XTC files from fortran90

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 1 09:21:30 CEST 2007

Hi Jones,

> I can already do that for .xtc files. Seems that, unfortunatelly, the least
> odd way is to find a way to get the last pieces of information needed
> (atomic charges and masses) from the .tpr files. Other ways would include
> lots of file translations, or adaptions in the codes themselves which would
> lead to "non-generality" of it.

I'd say the easiest is to get into gmx_editconf and look at the option
"-grasp" or "-mead" which put the atomic charge and vdw radius in the
b-factor and occupancy field of a .pdb file when given a .tpr file.
It's trivial to make it write charges and masses instead. Would also
be a good first exercise for C/Gromacs :p

> Sorry for not noticing the box shape in the .xtc file. I passed over that
> integer in the reading, dismissing it as only some kind of old feature
> useless now. Really sorry for that point.

I'm not sure what you mean with "shape" and "that integer". There's
nothing much redundant in the .xtc file and there are no integers
having to do with box shape. In fact, there is no "shape"...



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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