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

Darrell Koskinen darrellk at ece.ubc.ca
Sat Nov 7 01:06:56 CET 2009

Hi Mark,
I took a look at a tutorial where they perform an NPT simulation (http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf, page 11) and it appears to me that they simply ran the simulation with pressure and tempurature coupling "on" for a sufficient amount of time to reach equilibrium. 

I also searched in the GROMACS manual for NPT and came across the following:
/"The generally more useful Gibbs free energy G is related to the partition function
 of an N, p, T ensemble, which is assumed to be the equilibrium ensemble generated by a MD
simulation at constant pressure and temperature"./
This appears to indicate that in order to run an NPT simulation, we simply need to maintain constant temperature and pressure, which I assume simply means letting the system reach equilibrium, since, at equilibrium, the temnperature and pressure will be reasonably constant.

Please let me know if I am missing something.

Best regards,


Date: Fri, 06 Nov 2009 19:50:48 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Determining density of a gas in a simulation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4AF3E368.3060304 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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.


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