Dear Mark,<br><br>Thanks for your suggestions of including/using index file. This is fine but is it not a cumbersome process to define for different length of systems in this way! Since, one has to define/make the group for each carbonyl group with other pairs!<br>
<br>Anyway for the time being I am using this strategy. But if anyway has other options then kindly let me know.<br><br>Thanks in advance,<br>with warm regards,<br>anil<br>IIT Bombay<br>India<br>
<br><div class="gmail_quote">On Sun, Sep 13, 2009 at 9:41 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Anil Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Gmx Users,<br>
<br>
I need to calculate the H-Bonds of simulation trajectory with specification<br>
of i to i+2/3/4/5 so on..and i to i -2/3/4/5 so on...separately.<br>
<br>
Do anyone have any idea how to do this...since the present option g_hbond<br>
calculate both the hydrogen bonds together irrespective of i to i+/-<br>
2/3/4/5/6 and so on..<br>
<br>
Or is there any other program which can be used for this analysis.<br>
</blockquote>
<br></div>
Read g_hbond -h and/or consider creating suitable index groups with make_ndx in an index file to pass to g_hbond using -n.<br>
<br>
Mark<br>
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</blockquote></div><br>