Re: Simulation question

From: Gianluca Interlandi (
Date: Tue Jan 19 2010 - 13:18:58 CST

I would use BOX. If you use box, make sure that it is large enough in the
direction of pulling so that the protein does not see its own image even
after it gets extended. If you use sphere, make sure it is big enough so
that the protein is solvated at all times and never sees the finite
boundaries. I have seen studies where somebody has used a too small sphere
and the protein got desolvted once it was unfolded which in my opinion is
not good.


On Tue, 19 Jan 2010, snoze pa wrote:

> Dear NAMD users,
> Please suggest me which approach is better to start a SMD
> simulation. Water in BOX or Water in Sphere?
> Thank You.
> S

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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