Darrell Koskinen wrote:
Dear GROMACS Gurus,
I wanted to determine the density of the ammonia gas in my simulation
and compare this to the reference values and thought I could use
g_density for this purpose. I recall being told that I need to perform a
NPT simulation and achieve equilibrium. How do I perform an NPT
simulation? I assume this means that I fix the number of molecules, the
pressure, and the temperature. The number of molecules is definitely
fixed and I define the temperature in my .mdp file through
"ref_t =240 240". Is this the way in which to set the
temperature in an NPT simulation? I do not currently specify any
pressure in my simulation. Do I need to set the pressure as well through
a ref_p setting? And does the ref_p setting simply need to satisfy the
ideal gas equation for the specified N, T, & V?
P and T can't be "set". You can have an ensemble whose average over a
long period has a value. You can use an algorithm to move them closer to
a desired equilibrium value if the instantaneous one differs. See the
manual for more information. Doing some tutorial material and some
background reading sounds like a good idea, too.
And how do I determine when equilibrium is achieved? Should the
potential energy of the system or some other value stabilize to within
some deviation of the absolute value? If so, what would would be the
acceptable limit of this deviation ... 5% of the value? Other percentage?
It depends - there's no hard-and-fast rule and it will vary with which
observables you intend to measure.
Mark
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