Jarzynski's Equality relates work done during a process (e.g. steered molecular dynamics) to the Helmholtz free energy. I wonder if this requires my MD simulation to be NVT (not NPT)?
If I use constant pressure, could I simply change the Helmholtz free energy deltaF in the equality to Gibbs free energy deltaG?
I saw someone used this deltaG instead of deltaF in AFM experiments, but cannot find any computational papers using this modified version of Jarzynski's Equality.
Jarzynski identity holds for both NVT and NPT ensembles.
Here's the reference: http://dx.doi.org/10.1063/1.2338535
Jarzynski identity holds for both NVT and NPT ensembles.
Here's the reference: http://dx.doi.org/10.1063/1.2338535
Hi Yun,
just for trying to clearify. In a typical steered MD setup, you need two kind of simulation. With the first one you produce the initial microstates, while in the second ones you performe the properly called steered MD (where you collect the works done on the system). To address your question, if you are interested in recovering Helmhotz free energy, you have to sample the initial microstates in the NVT ensemble. If you rather want to get Gibbs free energy, you must sample the initial microstates accordingly (NPT). It doesn't matter in which ensemble you perform the steered transformations. This is clearly stated here: http://dx.doi.org/10.1063/1.2749257
Best regards,
Paolo
Hi Yun,
if your system is NpT-equilibrated, this means that you sampled initial microstates in that ensemble. Final microstates (the ones that you get at the end of the pulling simulations) could be associated with every ensemble (you can always think of adding thermostat and/or barostat and leave equilibrate the system without doing any work). What is really important is in which ensemble you equilibrate your system (of course constraining your control coordinate). So, if you did a NpT equilibration, you will get *Gibbs* free energy difference.
Best regards,
Paolo
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