[gmx-users] Understanding template.c

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 22 11:21:19 CEST 2010

On 22/04/2010 7:11 PM, Chandan Choudhury wrote:
> Hi gmx users !!
> I want to read the trajectory file (*.trr ), produced as a result of
> mdrun. I came to know that a file template.c already exists to facilate
> my process. I could compile and execute the template.c. Like
> printf("Atom name: %s\n",*(top.atoms.atomname[n]));
> printf("Atom charge: %f\n",top.atoms.atom[n].q);
> produces the Atom Name and the corresponding partial charges.
> respectively. I could also print the x, y, z coordinate for each frame
> present in the trr file.
> What am I  looking for is, how can I print the Atom number, Residue

They're probably also in the same data structure above - called "top". 
Search for its definition, and if necessary for the code where it is 
instantiated and filled with data.

> name, residue number? I was unable to find it in the program template.c.

Sure - it's a template. It doesn't relieve you of the need to search the 
codebase for actual information. :-)

> I would also like to know how do you prompt -s / -f / -n etc. option
> during executing gmx commands?

I'm not sure what you mean by "prompt". Pick a GROMACS tool that does 
something similar to what you want, use a debugger to step through it to 
see how the code works, then use that information to modify an existing 
tool, or create your own copying and pasting useful bits.


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