AMBER Archive (2008)

Subject: AMBER: velocity-verlet algorithm and ensembles

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Wed Oct 08 2008 - 13:59:46 CDT

 Dear All,
 
I want to use velocity-verlet algorithm for my MD simulations. And I searched Amber manuals and Amber mail archive in order to get more information about using  velocity-verlet ( rattle ) algorithm. But I only found some information about shake (  verlet ) algorithm. Mainly, which algorithms can be used in Amber 9/10 v. and how can I describe them in MD sander input files? Particularly, how can I describe velocity-verlet algorithm? Also Could you give me some information about using these integration algorithms with the right ensembles? For example I think that velocity-verlet algorithm should be used for NVE simulations.
 
Thanks in advance
 
 
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