Dear James,
I suggest with things like this that you follow articles in the literature
where people are having success at doing what you want. That's the best
source for good protocols, which methods to use and so on. Then use the
Amber email list for technical questions if things aren't working, or about
how to get things running when you already have a sense for what you're
trying to do. There's no real reason to think that the replies you get here
on which methods are "good" will come someone's experience with studying
systems similar to yours. That's what the literature is best at doing. Just
my advice...
carlos
On Sat, Jul 26, 2014 at 3:03 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> Dear Amber users!
>
>
> I wounder some detailes regarding the ussage of the Langeve\in's (ntt=3)
> thermostat in case when I simulate solvent implicitly (in my case with gb=8
> model). As I know initially Langevin's dynamics was the method for
> simulation of the implicit solvent (by modelling of collisions with the
> virtual particles) which can be used as the thermostat in cases when system
> is modelled with explicit solvent. Should I provide in input file higher
> values for gamma_ln in case of the application of the gb models or
> alternatively use another thermostat like Nose-Hover method?
>
>
> James
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Received on Sat Jul 26 2014 - 05:00:02 PDT
