Dear all,
I noticed that it is possible to freeze all the bonds around their
equilibrium distance when you use the serial version of sander and pmemd,
while only bonds containing hydrogen can be constrained with shake using
the parallel version. I know that other software like gromacs and namd allow
to freeze all bonds even in the parallel version. I wonder which is the
reason for this different choices, and if there is a computational advantage
in doing so, considering that freezing all bonds would allow the use of a
longer time step.
Thank you in advance
Stefano Pieraccini
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Received on Fri Nov 19 2010 - 07:00:04 PST
