[gmx-users] multi file input for index files

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 10 09:34:05 CET 2012

On 10/01/2012 7:13 PM, ahmet yıldırım wrote:
> Dear users,
> I created two different index files (A.ndx and B.ndx). I want to run 
> the two files at the same time.
> e.g.
> g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
> where, I want to calculate the hydrogen bonds between A and B.
> This command is giving the error as it expected. "Gromacs tools do not 
> support multi file input for index files" from 
> http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. 
> Is this correct? If no, what should I do?

You can put your two groups in the same index file.

Run make_ndx and quit to see the format for index.ndx that it generates 
by default. You can do that too.


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