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On 10/01/2012 7:45 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:CAKVtM2suNmXDHkp1mQNLOv2QkipKUdi3YGeNwKjbeRGMxiXCJQ@mail.gmail.com"
type="cite">Hi,<br>
<br>
<span lang="en"><span>But I want to calculate the hydrogen bonds
between A and B groups.</span></span> If I do as you said, I
will have calculated intra hydrogen bonds of a group AB (merged A
and B).<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKVtM2suNmXDHkp1mQNLOv2QkipKUdi3YGeNwKjbeRGMxiXCJQ@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">2012/1/10 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5">On 10/01/2012 7:13 PM, ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
<br>
I created two different index files (A.ndx and B.ndx). I
want to run the two files 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.
"Gromacs tools do not support multi file input for index
files" from <a moz-do-not-send="true"
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>
</blockquote>
<br>
</div>
</div>
You can put your two groups in the same index file.<br>
<br>
Run make_ndx and quit to see the format for index.ndx that it
generates by default. You can do that too.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark<br>
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</font></span></blockquote>
</div>
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<br>
-- <br>
Ahmet Yıldırım<br>
<br>
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