[AMBER] radial distribution function problem

From: Jio M <jiomm.yahoo.com>
Date: Sat, 4 May 2013 02:35:28 -0700 (PDT)

Dear All,

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. 
I have following doubts:

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.

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. Or it just confuses with some residue based approach?


regards,

Jiomm


lab mate 1, experimental guy, complains about desktop of lab mate 3: Why am not able to use numpad keys and have to turn ON NumLk always huh!
lab mate 2 computational guy: aaah! he must be 'an' AMBER user
)
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Received on Sat May 04 2013 - 03:00:03 PDT
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