[gmx-users] Reading XTC files from fortran90

[David van der Spoel]

Jones de Andrade wrote:
> Hi Mark.
> 
> Wait a second, you mean that editconf would allow me to have both 
> charges and masses on a .pdb file directly from command line (having 
> other matters asking for my presence absolutelly now, so please forgive 
> me if this message becomes somehow strange)
> 
> So, I would have atom names, number of molecules types, number of 
> molecules of each type, number of atoms of each molecule type, 
> coordinates, charges and masses on a .pdb file, correct?
no just atoms and charges.



> 
> But, still, where could I then easilly get the box type and sizes, as 
> well as simulation times?
box is in xtc file.

You could make your life easier by learning some C, unless you hae to 
link the trajectories to a big fortran library. By the way you can also 
trjconv -f k.xtc -o l.g87 which you can read using 10f8.3

> 
> Thanks a lot for all the help, and sorry for this punctual hurry here.
> 
> Sincerally yours,
> 
> Jones
> 
> On 9/30/07, *Mark Abraham* < Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     David van der Spoel wrote:
> 
>      > the box is in the xtc file, if you need the atom names a
>     corresponding
>      > pdb or gro file should do the trick. don't try to read tpr files or
>      > gmxdumps of it, that's a complete waste of time. you can e.g. use
>      > editconf to dump a pdb file with charges in the b-factor fields.
> 
>     Yes, I now see that editconf has that ability, and Jones can fill in the
>     masses himself, so he doesn't need to parse the .tpr at all.
> 
>      > And indeed, using fortran will make your life quite miserable for
>     these
>      > kind of things.
> 
>     :-)
> 
>     Mark
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se