[gmx-users] g_energy -fee -f2

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Sat Sep 20 01:50:02 CEST 2003

How does on run a trajectory using a tpr file from another trajectory?



On Thu, 2003-09-18 at 23:16, Anton Feenstra wrote:
> Xavier Periole wrote:
> > 
> > You ractually have to run two simulations. One would be the reference state
> > (A)
> > and the other is the perturbated state (B). g_energy calculate the free
> > energy difference
> > between the two states A and B. G_energy does not generate the perturbation.
> The way I have used this option is to look at free energy differences
> in conformations between a ground-state (GS) and excited-state (XS)
> fluorophore (FAD). In this case I ran two simulations, one with GS charges
> on the FAD, and one with XS charges. Then, I did four re-runs: GS trajectory
> with GS tpr, GS traj with XS tpr, XS traj with GS tpr and XS traj with FS tpr.
> (The 'GS traj/GS tpr' and 'XS traj/XS tpr' re-runs seem unnecessary, but
> there are slight differences in total energies calculated between 'original'
> and 're-run' that are elminated when all energies come from re-runs.)
> This gives an estimate of the delta-delta-G, i.e. the difference in free
> energy difference between two transitions (e.g., GS charges -> XS charges in
> one ensemble, or GS ens. -> XS ens. in one charge state).

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