Thank you for your reply. I will read the manual more carefully. <br><br><div class="gmail_quote">2012/6/5 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
<br>
On 6/5/12 4:40 AM, Turgay Cakmak wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi all,<br>
<br>
<br>
I would like to get information about *pi-pi stacking*, *van der Waals*,<br>
*electrostatic and hydrophobic interactions* for my system (several-peptides in<div class="im"><br>
a box filled with water). Can Gromacs compute these interactions?<br>
<br>
<br></div>
As far as I see from mailing-list, to get information on *hydrophobic<br>
interactions*, g_mindist and g_sas can be used. But, they look very different.<div class="im"><br>
Which one should be used?<br>
<br>
</div></blockquote>
<br>
Both. There are no Gromacs tools that magically do the analysis you're looking for, but combinations of available tools will. You can use g_mindist with a suitable index group to find hydrophobic contacts, and g_sas to compute hydrophobic and polar surface area. Other tools that can be useful for your other metrics are g_hbond, g_dist, and others. See the manual for a complete listing and decide what might be useful based on what you read there.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
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<br>
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>
<br>
==============================<u></u>==========<br>
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</font></span></blockquote></div><br>