Hey Mark
Using
[virtual_sitesn]
39 2 34 35 36 37 38
seems to be working to define virtual sites at COM of group of atoms.
thanks for the answer...
sikandar
On Mon, Apr 25, 2011 at 12:15 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 4/25/2011 2:49 PM, Sikandar Mashayak wrote:
Hi
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?
Table 5.6 says you choose a COM vsite with function type 2. So I expect
that
[virtual_sitesn]
39 2 34 35 36 37 38
will make atom 39 a vsite formed from the COM of atoms 34-38.
The manual is a bit deficient in this regard. Let us know how it goes, and
I'll update the manual.
Mark
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