On Sat, Feb 18, 2012 at 9:11 AM, Aron Broom <broomsday.gmail.com> wrote:
> I can't really imagine that the default would
> be 0 as that must mean a number of people think they are running langevin
> dynamics and are not, but that was my impression from the manual.
The default value for gamma_ln actually is 0. The 'ntt = 3' part of
the manual does call attention to this:
"Note that when <gamma> has its default value of zero, this is the
same as setting ntt = 0"
I suppose that when ntt=3 the code could set gamma_ln to something
automatically, but I think the reasoning behind leaving it at 0 is
that the 'best' value for gamma_ln changes depending on what you want
your thermostat to do. For GB simulations where you just want to add
some random friction to prevent "hotspots" while still having
relatively fast conformational sampling, a value of around 5 is
probably fine. If you need a collision frequency approaching that of
water you'll need something around 50-80. Of course, this also varies
depending on who you ask.
-Dan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 18 2012 - 08:00:02 PST
