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

[Sikandar Mashayak]

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.Abraham at anu.edu.au>wrote:

> 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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