[gmx-users] multi file input for index files

ahmet yıldırım ahmedo047 at gmail.com
Tue Jan 10 09:45:54 CET 2012


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).

2012/1/10 Mark Abraham <Mark.Abraham at anu.edu.au>

> 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<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 Yıldırım
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