AMBER Archive (2005)

Subject: AMBER: collision frequency in GBSA dynamics

From: Giulio Rastelli (rastelli.giulio_at_unimore.it)
Date: Tue Jan 25 2005 - 12:33:33 CST

Hi,
I am running a molecular dynamics calculation on a protein structure using GBSA
(igb=5, gbsa=1) using amber8. Using Langevin dynamics (ntt=3) one need to se
the collision frequency (gamma_ln) to something different from the default of
zero...what value of gamma_ln would be "appropriate" for this gb calculation?
Thanks for your help,
Giulio Rastelli

Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi, 183
41100 Modena
Italy

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