Re: water box size

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sun Nov 08 2009 - 07:57:36 CST

The size of the water box should depend on a couple of factors, and it
is probably better to think about the size of your protein in terms of
its spatial extent rather than the number of atoms (Imagine for
instance a long extended unfolded protein vs its compact folded form -
same number of atoms, but with different requirements on box size to
fully solvate them).

Next you have to think about what is going on with the periodic
boundary conditions and the cutoffs you are using. You don't want
your solute interacting with its periodic image.

It's probably worth taking a look at some basic textbooks on molecular
dynamics if you aren't familiar with these concepts.

Best wishes,
Josh

On Nov 8, 2009, at 8:23 AM, gurunath katagi wrote:

> 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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