Jones de Andrade wrote:
Hi all.
Firstly, thanks a lot for all the help! ;)
First, about reading the atom-names from a .gro file, I don't think it
would "so painfull". It would "look like" a bit to having a well
programmed "state machine" in the code.
About the language, yes, I admit that bor reads and writes, fortran is
miserable. But for calculations (like the inner codes of a certain
program? ;) only joking... :D ) if one chooses not to go by
assembly, fortran is still the way, specially if you consider the extra
simplicity of fortran90. Anyway, I would not even consider re-writing
the reads in fortran, but would love to consider to link to a library
(like in reading .xtc files) or gromacs compiled object just to read it
correctly. ;)
So now you have to weigh up the amount of time your computer will be
doing calculations (and then how much Fortran gains against the
alternatives) vs the amount of your time you'll spend writing and
debugging the I/O routines :-) Short of doing calculations whose cost is
on the order of more MD simulations, I'd be amazed if Fortran comes out
ahead.
About the box, is it on the .xtc file? Could not get the proper variable
of it, could someone give me some infor which is that?
Check out the C I/O routines?
Finally: yes, I considered changing everything to a .pdb file, despite
the file size and the fact that I completelly forgot it could have the
charges on it. But even so I would still have problems with the atomic
masses, am I right? Or can I put that on a standard pdb file with
gromacs programs?
You've got atom names in the pdb, so look the masses up in your own
code. Or post-process the pdb file to put masses in whichever of
occupancy and B-factor doesn't have charges.
Mark
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