SMD in water

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Jul 31 2008 - 06:22:43 CDT

A general question about SMD and water.
I've noticed in many articles that a protein is solvated and then SMD
simulations are used (one atom fixed, another is pulled) without any
boundary constraints.

Is there any specific reason besides having significantly smaller
number of water molecules?

I want to simulate a small peptide with SMD (so the number of waters
is not that important) and to use either cylindrical or spherical
boundary conditions. The N- and C-terminal CA atoms are supposed to be
pulled towards each other along parallel trajectories.

    Nterm------(force)------------------->
      \ ------
        --- / \ (peptide)
           \ / ---------
             ------- \
    <------------(force)-------------Cterm

Does this design have an advantage that the whole peptide is always
going to be at the center of either water sphere or water cylinder?
The reason i ask is because maybe someone have already done this and
ruled out this design as being not effective.

-- 
Roman Petrenko.
Physics Department
University of Cincinnati

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