water box size

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Sun Nov 08 2009 - 07:23:41 CST

Hi everyone..
Is there any criteria on as to what must be the size of the protein taking
the no. of residues and atom count ..
in the tutorial of ubiquitin, the atom count is around is 600 and have used
only 5 A water box so as to suit the learning requirement for a beginner..
But in practical, say if you have protein with some 600 residues with 9000
atoms, what will be the size of the protein ...
i.e is there any criteria in choosing the size of the water box for a
particulate no. of atoms or is it just based on the criteria that water box
must be suffficeintly large enough to
immerse the protein throughout the simulation...

thank you

-- 
Gurunath M Katagi
Graduate Research Student
Bio molecular computation Laboratory
Supercomputer Education & Research Center
Indian Institute Of Science, Bangalore- 560012
Karnataka State, India
Phone:080-22932737-319,080-22933061
email: gurunath_at_rishi.serc.iisc.ernet.in

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