[gmx-users] Reading XTC files from fortran90
Jones de Andrade
johannesrs at gmail.com
Mon Oct 1 19:01:30 CEST 2007
> I think those three can become yes in a really easy way: some kind of
> > "state machine" would easily do the trick and "count" them properly.
> Yes, but now you have to infer molecule changes from residue name
> changes, which is doable, but messy.
Forgot about this slice of the problem. You are right now, so, or a .ndx
file, or .tpr files. ;) Or read both residue counting and molecule
cou8nting from the .pdb file. ;)
> Only modifying editconf to print those in a adapted .pdb file, throw a
> > file conversion and much disk space "wasted". Or I can learn exactly
> > from editconf how to read it from .tpr or .top (I guess it takes from
> > these files the atomic charges when needed) and adapt into my codes.
> The point of editconf is to feed your system *one* pdb structure with
> atom names, charges and/or whatever - it would be easy to modify
> editconf to write masses in one column and charges in another. You rely
> on the user to then supply a .xtc file that corresponds to that .pdb, in
> the same way that most of the GROMACS analysis tools accept an .xtc and
> various subsets of the possible structure files. You don't convert your
> .xtc to a .pdb trajectory, because that would be immensely wasteful, and
> the static information of the names, masses and charges doesn't vary
> with time under the MD approximation.
Ops, now I've got your idea! I was thinking too much about trjconv way of
working instead of editconf one! Sorry!
On this way, yes, editconf becomes a really good idea, side-by-side with
reading the .tpr one. But, of course, and easier to implement one.
Thanks a lot for all information and for all your time. I'll start to look
into the sources you mentioned before and try to properly find out how to
deal with those problems properly. ;)
Thanks a lot again for all your time,
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