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<p>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.</p>
<p> </p>
<p>Jan</p>
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<div><font size="2" face="Arial">===========================================================</font></div>
<div><font size="2" face="Arial">Jan Marzinek<br>
PhD Candidate<br>
Centre for Process Systems Engineering<br>
Department of Chemical Engineering<br>
Imperial College London<br>
South Kensington Campus<br>
London SW7 2AZ<br>
E: </font><a href="mailto:j.marzinek10@imperial.ac.uk"><font size="2" face="Arial">j.marzinek10@imperial.ac.uk</font></a><br>
<font size="2" face="Arial">M: +44(0)7411 640 552</font></div>
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<div style="DIRECTION: ltr" id="divRpF142062"><font color="#000000" size="2" face="Tahoma"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of ahmet yıldırım [ahmedo047@gmail.com]<br>
<b>Sent:</b> Tuesday, January 10, 2012 8:13 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] multi file input for index files<br>
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<div>Dear users,<br>
<br>
I created two different index files (A.ndx and B.ndx). <span id="result_box" lang="en" class="short_text">
<span class="hps">I want to run</span> <span class="hps">the two files</span> <span class="hps">
at the same time.<br>
e.g.<br>
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx<br>
where, I want to calculate the hydrogen bonds between A and B.<br>
This command is giving the error as it expected. "</span></span>Gromacs tools do not support multi file input for index files" from
<a href="http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html" target="_blank">
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html</a>. Is this correct? If no, what should I do?<br>
<br>
Thanks in advance<br>
-- <br>
Ahmet Yıldırım<br>
<br>
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