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
