On 6/05/2011 10:17 PM, Gavin Melaugh wrote:
Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site when I stated that it was to be at the
COG of the 3 atoms in the [virtual_sitesn] directive.
Yes it does, but (IIRC) the implementation requires that each of the
constructing atoms and the virtual atom(s) are distinct atoms. mdrun
does the book-keeping to know which atoms are sensible at different
stages of the integration. So the input coordinate file needs to have
such atoms there, but I rather suspect their coordinates will get
ignored - that's easily tested, of course.
Mark
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Justin
I have tried this but I am now getting different errors. I take it that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?
Virtual sites are included in all the force fields already, but if you
want some custom name, then yes, include them in a new [atomtypes]
directive. I see no reason to create three distinct, but identical,
types as you have.
I index the virtual sites in the atoms directive in accordance with the
rest of the molecule. atom numbers go from 1-228, therefore I label the
3 virtual sites 229 to231.
The error I get now is
Atom index (229) in virtual_sites3 out of bounds (1-228).
This probably means that you have inserted topology section
"virtual_sites3"
in a part belonging to a different molecule than you intended to.
In that case move the "virtual_sites3" section to the right molecule.
Do I have to have the virtual sites in the gro file also? This doesn't
make sense
Yes, you need their coordinates as part of the initial state.
-Justin
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