From: Grant Schauer (grantschauer_at_gmail.com)
Date: Sat Mar 24 2012 - 17:08:55 CDT
When choosing good E and alpha (accelMDE and accelMDalpha) values for an
accelMD run (dihedral boost only), what value do I use as my potential
For choosing E, Hamelberg, Mongan, and McCammon suggest in J.Chem.Phys
2004 to use an E greater than <V>, the average potential from the starting
structure. So when I'm only modifying the dihedral potential (accelMDdihe
on), I take this to mean the average dihedral energy from the output file
as evaluated during energy minimization- is this correct?
For choosing alpha, they also suggest to use alpha=E-<V>. So if the
average dihedral energy from the first 100 minimization steps is ~1500, and
I want an an alpha for fairly aggressive sampling, does E= 1600 and
alpha=100 seem like a reasonable starting point? Or is it important to
scale alpha to the size of my system as suggested here:
Any advice would be helpful, thanks.
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