Hi,
On Sat, May 4, 2013 at 3:35 AM, Jio M <jiomm.yahoo.com> wrote:
> I am using radial distribution function for water and ions in ptraj. When I use say a bin size around 0.6 I dont get exact number of water atoms (rather few more than expected; for my cases it varied from 4 to 20 extra water molecules (that is 12 to 60 atoms extra). But when I use a bin size 0.1 or 0.01 I get more closer and even exact number of water atoms.
It's not clear to me why you are expecting a specific number of water
molecules than what the 'radial' command indicates. Does it not agree
with a separate RDF calculation you have performed? It would be
helpful if you could provide the exact ptraj input and some more
details about your system. RDF calculations with different bin
spacings should agree qualitatively, but when you change the size of
the volume slices you should definitely expect some variation,
particularly in the closer volume slices where there are typically
less data points. The RDF will also be more sensitive to bin spacing
if you are using a small number of input trajectory frames.
> 1) Though it makes no sense but still I want to ask: does ptraj consider as a point atom or atom having radii? If radii ofcourse it will fragment the atom even! in adjacent shells.
The 'radial' command in ptraj/cpptraj bins atoms as points.
> 2) Why ptraj over counts the atoms? I mean to say it should not matter if programme creates a number of shells with 0.6 or 0.1 thickness then it should provide total number of atoms to be same.
I don't think this is true. Just like you wouldn't expect a simple 1-D
histogram with a bin spacing of 1.0 to look exactly the same as a
histogram with a spacing of 0.1. Again, they will agree qualitatively,
but the exact representation will depend to an extent on how the data
is partitioned. This is particularly true for RDFs due to the
normalization.
-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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 04 2013 - 09:30:03 PDT
