[gmx-users] Reading XTC files from fortran90

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 1 18:35:49 CEST 2007

Jones de Andrade wrote:

>  >From .gro or .pdb file in the standard way.
>      > number of molecules types,
>     No
>      > number of molecules of each type,
>     No
>      > number of atoms of each molecule type,
>     No
> 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.

>      > coordinates,
>     Yes
>  From .xtc or .pdb file.
>     charges
>     Yes, if you use the right editconf option
>     and masses on a .pdb file, correct?
>     No.
> 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.

>     If you use the editconf suggestion to get charges, you don't need to
>     read a .tpr file.
> But then or I get locked into the problem of generality of having too 
> much disk usage. But that idea will be also usefull to learn how to read 
> the masses and charges from .tpr files.

Easier is to hack editconf as described above.


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