Re: Accelerated MD in NAMD

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Nov 07 2013 - 09:59:39 CST

> 3. You might also find this paper interesting:
> http://www.pnas.org/content/110/27/10982.full
> 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:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/1718.html

thanks,
Thomas

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/

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