Thank you so much!
On 6 September 2016 at 21:41, David A Case <david.case.rutgers.edu> wrote:
> On Fri, Sep 02, 2016, Dd H wrote:
>
> > I want to do a MD simulation with a protein in explicit water model. And
> I
> > have to choose a thermostat for temperature regulation. So which is the
> > best thermostat for my system? Moreover, which barostat should I use?
>
> I recognize that the manual perhaps makes these things more complex that
> they need to be.
>
> The most widely-used thermostat for Amber users, by far, is ntt=3. This
> should generally be accompanied by a smallish friction, say gamma_ln=5.
> (Some people use even smaller frictions.) Be sure to set ig=-1, or use
> some other scheme to prevent re-use of the random number seed on restarts.
>
> Note that all thermostats interrupt Newton's equations of motion: if you
> are
> interested in dyanmical behavior, you really should be running NVE
> simulations
> (generally following NTP equilibration to get a system with the proper
> density.) If you are just interested in *qualitative* dynamical behavior,
> a Langevin thermostat with small gamma_ln may suffice.
>
> The Monte Carlo barostat is both computationally efficient and samples
> the canonical NTP ensemble. The older, "Berendsen" barostat, suppresses
> volume fluctuations, but is still often used.
>
> Opinions on this subject vary a lot, and others may wish to pitch in.
>
> ...dac
>
>
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Received on Tue Sep 06 2016 - 19:30:03 PDT
