From: Thomas Albers (talbers_at_binghamton.edu)
Date: Wed Aug 29 2012 - 15:06:04 CDT
Does anyone on this list perhaps have experience with accelerated MD?
We are looking at a short peptide in a membrane (30000 atoms total)
and are trying to find suitable values for E and alpha in dual-boost
Here are the relevant average energies (kcal/mol) for classical MD:
dihedral 4070.72, total -42381.53
With accelerated MD we see:
dihedral 6362.78, total -40156.92
The dihedral energy is higher, as expected, because the system
explores a greater amount of phase space, but it seems that the
contribution to the increase in total energy comes almost exclusively
from the dihedral energy. If I read this right there is almost no
boost at all applied to the diffusive degrees of freedom. Am I
understanding the data right?
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