[gmx-users] g_energy -fee -f2

[Ilya Chorny]

That doesn't make any sense. I need to sample the perturbed state(B)
while I'm on state A in order to d FEP. How is that possible with with
two different trajectories. Would it not be easier just to print the
perturbed energy in out mdrun output.

Thanks,

Ilya



On Thu, 2003-09-18 at 09:30, 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.
> 
> XAvier
> 
> 
> ----- Original Message -----
> From: "Ilya Chorny" <ichorny at maxwell.compbio.ucsf.edu>
> To: <gmx-users at gromacs.org>
> Sent: Thursday, September 18, 2003 12:17 PM
> Subject: [gmx-users] g_energy -fee -f2
> 
> 
> > How does one generate a second energy file for the -f2 option with
> perturbed
> > energies for FEP calculation?
> >
> > Ilya
> >
> >
> >
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Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
Postdoctoral Researcher   University of California-San Francisco
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