Dear all,
there is probably some "scaling problem" in "radial" function/action of
the cpptraj.
Let's suppose that I have residuum CEN which is composed of one atom only.
If I understood well the description of the "radial" function ( page 189
of the AT manual ),
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 found that
WAT_CEN.RDF = 19902.06294 * WAT_gCEN.RDF
Similarly these two commands
radial Cl_CEN.RDF 0.2 30.0 :Cl- :CEN
noimage
radial Cl_gCEN.RDF 0.2 30.0 :CEN :Cl-
noimage center1
should also provide identical results, instead I found that
Cl_CEN.RDF = 1.992481203 * Cl_gCEN.RDF
So i) the pairs of functions which should be identical differ by some
multiplicative constant and ii) moreover this multiplicative constant is
different for different cases (e.g. 19902.06294 in WAT case, 1.992481203
in case of Cl- ...).
I am using Amber12/AT12 with all patches up to now.
Thanks in advance for the explanation.
Best wishes,
Marek
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 31 2013 - 16:30:03 PST
