On Mon, Sep 26, 2011, Adrian Roitberg wrote:
> Well, for starters, did you change the compressibility value when you
> run your simulations ? The default value in amber is for water, so you
> need to change it in the input.
The compressibility value in sander/pmemd only affects the rate at which the
system comes to equilibrium; the magnitude of the pressure fluctations should
be independent of this choice. Given that the value to taup is pretty
arbitrary anyway (assuming is is large enough, say >= 1 ps), changing it for
different liquids is rather a matter of taste.
>
> In any case, all solids and most liquids are incompressible as a general
> rule.
incompressible -> nearly incompressible
>>> We found that at the first run (of 500 ps) the average pressure lead to a
>>> high value. In the following runs this value rise fluctuating between 0.6 -
>>> 1.7 (the average) this value don't reach 1 even after 50 ns of running.
This is expected; see, e.g.
http://ambermd.org/Questions/pressure.html
...dac
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Received on Mon Sep 26 2011 - 19:30:04 PDT
