Hi,
On Thu, Jan 31, 2013 at 4:47 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> these two commands
>
> radial WAT_CEN.RDF 0.2 30.0 :WAT :CEN noimage
> radial WAT_gCEN.RDF 0.2 30.0 :CEN :WAT noimage center1
>
> should provide identical results (i.e. WAT_CEN.RDF=WAT_gCEN.RDF ), instead
I don't think that's correct. In the first command you are computing
the RDF of the atoms in every WAT residue to the atoms in CEN
residue(s). However, in the second command you are computing the RDF
of the geometric center (i.e. a single point) of the CEN residue(s) to
the atoms in every WAT residue. Also, note that the default density
value is 0.033456 molecules/Ang^3 which corresponds to a density of
water approximately equal to 1.0 g/mL; if you're calculating something
different you need to adjust (or just use the 'volume' keyword) if
your system has periodic box info. For example, when you're
calculating :CEN to :WAT you're calculating 3 distances to each water
(O and 2 Hs) instead of 1 so the density value would need to be
adjusted appropriately with the 'density <density>' keyword.
Hope this is helpful,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Jan 31 2013 - 21:00:02 PST
