If the thermostat is thermodynamically sound, it will not affect
hydrophobicity. .DaveCase That's very surprising about the Berendsen even
corrupting simulations at low strength. Never again. Should we going to
deprecate the feature in the code?
On Wed, Nov 23, 2016 at 3:14 AM, Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> wrote:
> Thank you very much for your help.
>
> We have tested the Berendsen thermostat, but in MD of a similar system we
> observed the "flying ice cube" effect. So we've change the thermostat to
> Langevin with gamma_ln value of 1.0. I'll check the smaller value.
>
> And what about the hydrophobic properties of amino acids? Does the
> thermostat affect these properties?
>
> I really appreciate your help :)
> Have a nice day!
> Karolina
>
> W dniu środa, 23 listopada 2016 David A Case <david.case.rutgers.edu>
> napisał(a):
>
> > On Tue, Nov 22, 2016, Dave Cerutti wrote:
> >
> > > Yes, fair enough--Berendsen is bad, I'm with Bernie (Brooks)! A very
> > weak
> > > Berendsen thermostat is what was recommended to me for simulations
> where
> > > diffusion properties and NVT are needed simultaneously, by one of our
> > > respected colleagues no less. And, I agree--formally, it's bad, but
> with
> > > weak thermocoupling, in practice the effects are negligible.
> >
> > In the bad old days, we used Berdensen and got "flying blocks of ice".
> We
> > found that by tightening up tolerances one could more or less get rid of
> > this. But that was for runs of dozens of nanoseconds. I recently
> thought
> > I could use a weak Berdensen thermostat just to keep the overall energy
> > from drifting. Seemed to work great for about 8 microseconds, at which
> > point the protein froze--just like the old days, but now after 100 times
> > longer simulation. Rules of thumb that seemed good for simulations of
> > 10^7 steps may fail for runs of 10^10 steps.
> >
> > I suspect (following work from Leimkuhler, Izaguirre, Skeel, etc.) that
> > Langevin with a really good random number generator and a very low
> > collision
> > constant would have been a better choice for me. But I don't have
> personal
> > experience to back that up.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 23 2016 - 08:00:04 PST
