Hi Brian,
>It is probably worth mentioning that pressure control in AMBER uses the
>Berendsen barostat, which does NOT produce the NpT ensemble. Much like the
>Berendsen thermostat, it merely keeps the related microscopic quantity
>near
>the target value, but does not generate the correct distribution. This is
>perfectly adequate for generating sensible densities near the NpT average
>and is thus fine for equilibration, but I would not recommend using it for
>long production runs, especially if you are interested in fluctuations
>(they will simply be wrong).
Do you have evidence, or a citation for this conclusion? It is certainly
known to be true that the Berendsen thermostat does not correctly maintain
a gaussian distribution of velocities for a system that is not well
equilibrated already. However, I am not sure the same is true for the
barostat. If you could explain your reasoning here and the evidence you
have for not using it for long production runs I'd be very interested to
hear it. We are considering adding additional barostats into AMBER but
first I want to establish precisely what it is that people see is wrong
with a Berendsen barostat over say a langevin piston.
Thanks,
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Thu Mar 07 2013 - 20:30:02 PST
