[gmx-users] virtual sites set up for topology file

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> Thanks for the reply. To create a virtual site at the centre of geometry
> of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
> the index of the site, the index of the three atoms and then the
> function type 1 which determines that it is COG.

OK, so that would seem to be right from Table 5.6, but it's not discussed 
anywhere else, so I suspect that it may be a feature that either got broken 
along the way, or for some other reason doesn't work, since it's not :)

> Or as I now realise. State [virtual_site3], site index atom indices, and
> function 1. The fact that there are no parameters then by default must
> mean it is COG. Is this correct?
> 

I don't know if [virtual_sites3] can be specified without any parameters.  It 
seems to me that this shouldn't be correct.  It never hurts to try.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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