Thanks Carlos!
Hovewer my question was rather to some general case
e.g in DNA Tutorial (in part where we use implicit solvent) I've found
10-mer DNA MD Generalized Born, 12 angstrom cut off
&cntrl
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 100000, dt = 0.001,
cut = 12.0
/
In the above in file, it can be seen that langeven's thermostat (with the
same gamma_ln as in case of the explicit solvent) is generally applicable
with the GB models. My doubts are regarding gamma_ln = 1.0 value used in
such simulation. In my opinion this value might be bigger e.g (50) in case
of implicit solvent because in such systems we lack for viscous (water)
medium that might be compensated by the increasing friction (which are
result of the collision with virtual particles) what are langevens dynamics
in fact should do. Does this assumpions true or not?
*James*
2014-07-26 15:50 GMT+04:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jul 28 2014 - 04:30:02 PDT
