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

Darrell Koskinen darrellk at ece.ubc.ca
Fri Nov 6 09:33:52 CET 2009

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?

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?



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