On Fri, Jan 15, 2010, Andrew Voronkov wrote:
>
> EPSIN = 3.0
> http://peds.oxfordjournals.org/cgi/reprint/2/3/177
You can try this, but there a seemingly good reasons that the Amber developers
consider this a dangerous idea.
Generally, we chose defaults for Amber carefully, trying to steer people in
well-tested directions. Amber is a research tool, and we certainly encourage
people to experiment. But I would recommend against just looking at every
possible option and picking one out of the air that sounds good. The paper
you cite has nothing to do with GB simulations.
> gamma_ln = 5.0
> tautp=5.0
For GB simulations, we recommend a Langevin thermostat; in such a case, tautp
is irrelevant.
> saltcon = 0.15
I don't know much about the mm-pbsa scripts you are using, but it sounds like
"saltcon" and "ISTRING" are same thing.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 15 2010 - 09:30:03 PST
