Re: Accelerated MD in NAMD

From: Thomas Evangelidis (
Date: Thu Nov 07 2013 - 09:59:39 CST

> 3. You might also find this paper interesting:
> There is some discussion in the SI about choosing aMD parameters for a
> dual-boost setup for a different GPCR that may be helpful.
> Very good one! The first one I see to implement dual-boost aMD on the
whole protein-membrane system. The authors introduce a different empirical
rule to choose dihedral Energy cutoff and alpha value, but use the old rule
for the total Potential Energy threshold and the respective alpha:

Edihed = Vdihed_avg + lamda*Vdihed_avg
ádihed= lamda*Vdihed_avg/5
Etotal = Vtotal_avg + 0.2*Natoms
á total = 0.2*Natoms

Jeff, since you are very familiar with the physics behind aMD and its
effects on system dynamics, I wonder if you could comment on my recent post
about combination of aMD with an external electric field:


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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