> On Nov 23, 2016, at 10:48 AM, David Cerutti <dscerutti.gmail.com> wrote:
>
> 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?
>
I think we should add a big warning rather than deprecating it. (e.g: for reproducibility)
Hai
>
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 23 2016 - 08:00:05 PST
