[gmx-users] multi file input for index files
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:
> 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.
> 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
> 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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> Ahmet Y?ld?r?m
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