[gmx-users] multi file input for index files

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Tue Jan 10 09:33:57 CET 2012

So as you can see Gromacs does not support multi file input :) Create one index file and specify there your two groups. Then g_hbond will ask you to choose two groups from this file.


Jan Marzinek
PhD Candidate
Centre for Process Systems Engineering
Department of Chemical Engineering
Imperial College London
South Kensington Campus
London SW7 2AZ
E: j.marzinek10 at imperial.ac.uk<mailto:j.marzinek10 at imperial.ac.uk>
M: +44(0)7411 640 552
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of ahmet yıldırım [ahmedo047 at gmail.com]
Sent: Tuesday, January 10, 2012 8:13 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] multi file input for index files

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 http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. Is this correct? If no, what should I do?

Thanks in advance
Ahmet Yıldırım

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120110/3a676a4c/attachment.html>

More information about the gromacs.org_gmx-users mailing list