On Mon, Oct 11, 2010, Ben Roberts wrote:
>
> The other problem is that as well as pconv, both sander and pmemd define
> and use a "pressure_constant", which, unlike pconv, is a conversion
> factor appropriate for atmospheres. In sander's runmd, at least, this
> value is only used to calculate ener%pres(4), whatever that is, and even
> then only if iamoeba is non-zero and ipimd is zero. Can anyone clarify
> for me why this particular combination would use atms instead of bars
> for pressure, and whether I should fix it? As far as I can tell, this
> "feature" is also present in pmemd.
ener%pres(4) is 1/3 the trace of the pressure tensor; it is compared
to the reference pressure to run the Berendsen pressure coupling. I
don't understand why pconv is used for Amber ff and pressure_constant
for amoeba...sounds like someone was trying to exactly match tinker.
I've updated the manual to clarify what pres0 does. The amoeba section of the
code should work the same as the rest; presumably this means that
pressure_constant should go away.
....dac
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Received on Mon Oct 11 2010 - 20:00:03 PDT
