> PRESS is never 1. Is PRESS presented here in atm or other units.
Substantial pressure fluctuations are expected when using pressure
control (NPT); the *average* should be close to the target pressure.
There is a lot about this in the Amber reflector archive. To my
knowledge, PRESS is in atm units.
> Should I conclude that
>
> 1) my dynamics conditions are not simulating natural environment which gives density of 1.3266 of solvent only
>
> or
>
> 2) should I say my macromolecule is making empty pockets within itself
> (I can see them) which makes system less dense as compared to the
> otherwise condition of whole system was made of dcm solvent only of
> same volume.
It sounds like these conclusions are not mutually exclusive. I would
be very suspicious of "empty pockets" within a macromolecule,
especially if they have developed during equilibration. (I have not
followed your previous posts carefully enough to know where you are in
the simulations.) If there are potential problems with your solvent,
I would not assume such pockets to be biologically meaningful.
You may want to try reproducing the known solvent density by running a
"control" simulation following your current protocol but with solvent
only (no macromolecule).
Sally
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Received on Sat Nov 21 2009 - 23:00:02 PST
