The "hot solvent, cold protein" problem is a Berendsen thermostat issue, as
is the "flying ice cube." That's ntt = 1. If you use the Andersen or
Langevin thermostats (ntt = 2 or 3, respectively) I think you'r ein better
shape, although perusing the literature suggests that this hot/cold
partitioning is more insidious than I had thought. It seems that the thing
to do is use as weak a thermostat as you can, to minimize the
thermocoupling that gives rise to the temperature gradient between
components of your system.
Dave
On Wed, May 8, 2019 at 2:52 AM Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> wrote:
> Dear Amber Users,
>
> I'm curious how is pmemd or sander dealing with the thermostat of the whole
> system.
> I've recently read about the hot solvent, cold solute problem and would
> like to ask, if it is possible in either sander or pmemd to check the
> temperature separately for the protein and the solvent?
> And is it possible to set the thermostat separately for the protein and the
> solvent?
> How can I be sure that I'm not having a cold protein surrounded by hot
> water?
>
> I'm looking forward for some more knowledge!
> Best regards,
> Karolina Mitusińska
> PhD student
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Received on Wed May 08 2019 - 00:30:01 PDT
