I can't keep my pulling directions the same with the SMD vector

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
calculations.
Best,
Mert

Free energy calculation from steered molecular dynamics simulations using
Jarzynski's equality Park,
Sanghyun<http://adsabs.harvard.edu/cgi-bin/author_form?author=Park,+S&fullauthor=Park,%20Sanghyun&charset=UTF-8&db_key=PHY>;
Khalili-Araghi,
Fatemeh<http://adsabs.harvard.edu/cgi-bin/author_form?author=Khalili-Araghi,+F&fullauthor=Khalili-Araghi,%20Fatemeh&charset=UTF-8&db_key=PHY>;
Tajkhorshid, Emad<http://adsabs.harvard.edu/cgi-bin/author_form?author=Tajkhorshid,+E&fullauthor=Tajkhorshid,%20Emad&charset=UTF-8&db_key=PHY>;
Schulten, Klaus<http://adsabs.harvard.edu/cgi-bin/author_form?author=Schulten,+K&fullauthor=Schulten,%20Klaus&charset=UTF-8&db_key=PHY>

http://adsabs.harvard.edu/abs/2003JChPh.119.3559P

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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