<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>21 maj 2012 kl. 06.54 skrev Anirban:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><br><div class="gmail_quote">On Mon, May 21, 2012 at 3:09 AM, mu xiaojia <span dir="ltr"><<a href="mailto:muxiaojia2010@gmail.com" target="_blank">muxiaojia2010@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks for prompt answering but I may need to clarify my question and sorry for the understanding,<div><br></div><div>For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different dipeptides instead of counting all the possible h bonds between Ala(intermolecularly and intramolecularly)<br>
<br></div></blockquote><div><br></div><div>Make two groups with make_ndx that contains the residue numbers (or specific atom numbers) of the ALA residues between which you want to count the H bonds and then select these group numbers with g_hbond.</div>
<div><br></div><div>-Anirban</div></div></blockquote><br>And if you have many alanines you might have to call g_hbond many times (think in the lines of scripting). Or invoke g_hbond once with the index group consisting of all alanines chosen twice and decompose the hbonding matrix (-hbm -hbn) yourself (python/perl).</div><div><br></div><div>Best,</div><div><br></div><div>Erik</div><div><br><blockquote type="cite"><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div></div><div>Thanks very much!</div><div class="HOEnZb"><div class="h5">
<div><br></div><div><br><div class="gmail_quote">On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><br>
<br>
On 5/18/12 7:22 PM, mu xiaojia wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi gmx-users,<br>
<br>
I have a question might be explained before but I cannot understand from the<br>
previous , how to calculation the intermolecular h-bonds between two molecules?<br>
I saw someone mentioned using a second tpr file, but how to do it specifically?<br>
Thanks very much!<br>
<br>
</blockquote>
<br></div></div>
g_hbond asks for two index groups to be selected. Assign each molecule to an index group and select them when prompted.<br>
<br>
-Justin<span><font color="#888888"><br>
<br>
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Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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