[gmx-developers] Energy analysis

Berk Hess hess at kth.se
Wed May 7 17:53:37 CEST 2014

On 05/07/2014 05:31 PM, Shirts, Michael R. (mrs5pt) wrote:
>> - the free energy estimate code
> yes
>> or whether I can drop those?
> So I would vote for not dropping them.
> Berk, by using the free energy estimate code, do you mean g_bar, or the
> single pass free energy estimate described on page 274 (D.31) of the
> manual (Actually, looking at 4.5.6 of the manual).  Just to clarify.
I was thinking of free-energy perturbation. Now I don't recall how I 
actually did that. But I guess you would rerun a trajectory produced 
with hamiltonian A with hamiltonian B. Then you can use g_energy with 
two energy files.

> Eventually, it seems like there should be one process (either single pass,
> or g_bar, but not both).  Actually, it would be best to put it in an MBAR
> context, but that's on me . . .

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