AMBER Archive (2004)

Subject: Re: AMBER: Free energy in Amber8

From: Miguel (miguel_at_qorws1.uab.es)
Date: Tue Jun 01 2004 - 06:11:39 CDT

 Hello, all

> One futher question - how much time for the MD is generally considered to be good for each of the clamda vales. (say 100 ps etc) ?
>

 Well, I'm still using amber 7 and Gibbs, but I would say that the apropiate lenght of the MD run at each lambda depends on the size and movement freedom of your system. There are no "universal conditions", as the energy surface of big systems is much harder to explore representatively.

 I'm running TI calculations of a cyclodextryin catenane using 500 ps of MD per lambda value...

 Miguel de Federico.
 
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