[gmx-users] multi file input for index files

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 10 09:48:58 CET 2012

On 10/01/2012 7:45 PM, ahmet y?ld?r?m wrote:
> Hi,
> But I want to calculate the hydrogen bonds between A and B groups. If 
> I do as you said, I will have calculated intra hydrogen bonds of a 
> group AB (merged A and B).

I didn't say to combine your groups. I said to put both group 
definitions in the same file. Have you looked at the example I 
suggested? Those groups are in the same file and yet distinct.


> 2012/1/10 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>     On 10/01/2012 7:13 PM, ahmet y?ld?r?m 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.
>     Mark
>     -- 
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> -- 
> Ahmet Y?ld?r?m

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