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unit for the harmonic potential in the Desmond .cms file
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Rasmus Leth  
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 More options Aug 9 2012, 1:37 pm
From: Rasmus Leth <rasmuslet...@gmail.com>
Date: Thu, 9 Aug 2012 10:37:36 -0700 (PDT)
Local: Thurs, Aug 9 2012 1:37 pm
Subject: unit for the harmonic potential in the Desmond .cms file
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Hi All

I am wondering what unit the atombond hamonic potential in the Desmond .cms
file is? The bond definitions in the file can be found by searching for
"ffio_bonds" in the .cms file if opened as a text document. There you will
find the specific atoms, bondlenghts and the bondstrength is the last value
in each string (line of text). The bond strenght defined by Desmond is
usually in the range of 340, which is somewhat similar to the strenght of a
covalent bond measured in kJ/mol. My question is whether I can be sure if
the unit for the values in the .cms file is actually kJ/mol of if it is
something else?

Thank you,
Rasmus


 
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James Watney  
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 More options Aug 10 2012, 5:42 pm
From: James Watney <jwat...@gmail.com>
Date: Fri, 10 Aug 2012 14:42:11 -0700 (PDT)
Local: Fri, Aug 10 2012 5:42 pm
Subject: Re: unit for the harmonic potential in the Desmond .cms file
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Desmond energies are given in kcal/mol.  The harmonic force constants in
the .cms file are therefore given in kcal/mol/ang^2

Best,

James


 
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