[gmx-users] Determining density of a gas in a simulation

[Mark Abraham]

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