Hey Mark<div><br></div><div>Using </div><div><br></div><div><meta charset="utf-8">[virtual_sitesn]<br>39 2 34 35 36 37 38</div><div><br></div><div>seems to be working to define virtual sites at COM of group of atoms.</div>
<div><br></div><div>thanks for the answer...</div><div><br></div><div>sikandar<br><br><div class="gmail_quote">On Mon, Apr 25, 2011 at 12:15 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 4/25/2011 2:49 PM, Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I am not sure , even after reading the manual, about how to specify virtual site in topology file which is located at com of 5 atoms. If I were to specify it by using [ virutal_sitesn] then how to specify weights, so that vsite is at COM?<br>
</blockquote>
<br></div>
Table 5.6 says you choose a COM vsite with function type 2. So I expect that<br>
<br>
[virtual_sitesn]<br>
39 2 34 35 36 37 38<br>
<br>
will make atom 39 a vsite formed from the COM of atoms 34-38.<br>
<br>
The manual is a bit deficient in this regard. Let us know how it goes, and I'll update the manual.<br>
<br>
Mark<br><font color="#888888">
<br>
<br>
<br>
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