[gmx-users] Virtual site at COM of more than 4 atoms

[Mark Abraham]

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