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

Justin A. Lemkul jalemkul at vt.edu
Fri May 6 13:45:45 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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