Thank you very much for who have replied. I have another quick question: when AMBER calculates the temperature of a system which has atoms frozen or restrained, does these frozen or restrained atoms are still counted? Thanks!
> On Apr 2, 2017, at 12:04 PM, David Case <david.case.rutgers.edu> wrote:
>
> On Sun, Apr 02, 2017, Michael R Shirts wrote:
>>
>> In the limit of long enough time, the temperature distribution of
>> Andersen is indeed the canonical distribution.
>
> Just a few quick points, from very much a non-expert:
>
> 1. The ntt=2 option in Amber is rather different from the thermostat
> proposed by Andersen in 1980. (The upcoming Amber 2017 Reference
> Manual will be revised to make this clearer.) In Amber, setting
> ntt=2 simply automates the process of running as series of NVE
> simulations, starting from the coordinates at the end of the previous
> simulation, and velocities chosen from a Maxwell-Boltzmann distribution
> at the desired temperature.
>
> 2. As Leimkuhler and Matthews emphasize in their book "Molecular
> Dynamics", the rate and degree to which coordinates sample a canonical
> distribution can be quite independent of the rate and degree to which
> the momenta are correctly sampled. Most simulations in our field (say
> for free energy estimation) rely more heavily on getting the proper
> distribution of conformations than on the proper distribution of
> momemta.
>
> A well-known example of this arises for various flavors of Langevin
> dynamics schemes when applied to a harmonic oscillator. With a finite
> time step you can get the correct distribution of coordinates, or the
> correct distribution of momenta, but not both at the same time.
>
> 3. "Proofs" that a given thermostat yields (or fails to yield) a canonical
> distribution generally assume that the dynamics is propagated correctly,
> which will not be true with finite time steps. Numerical tests, like
> those described by Michael Shirts, or against "gold standard" simulations
> run with very small time steps, are generally required for any practical
> integration protocol.
>
> ....dac
>
>
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Received on Tue Apr 04 2017 - 10:30:02 PDT
