From: Mert Gür (gurmert_at_gmail.com)
Date: Sun Apr 19 2009 - 07:56:00 CDT
I try to evaluate th PMF of unbinding of a protein-protein complex. As was
suggested for SMD calculations in the following paper, I try to move only
into the x direction. But I just can't keep my reaction coordinates (which
is the vector between the fixed atoms and smd atoms) along the x direction.
I also tried to aplly an external constraining force of 1/10 in magnitude of
the SMD spring constant. But after each simulation the vector keeps
increasing its y magnitude.
So my question here is how high can I go with these constraining forces so
that my reaction coordinate moves strictly along the x direction and still
makes sense. Or is there any other methodology I missed. I tried to follow
all the discussion that have been performed previously regarding the SMD
Free energy calculation from steered molecular dynamics simulations using
Jarzynski's equality Park,
where it is indicated that:
"In the simulation, we fix one end of the molecule ~the N atom of the first
residue! at the origin and constrain the other end ~the capping N atom at
the C-terminus! to move only along the z axis, thereby removing the
irrelevant degrees of freedom, i.e., overall translation and rotation"
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