[gmx-users] Energy profile with umbrella sampling
pimlists at googlemail.com
Wed Jul 12 14:30:04 CEST 2006
On 7/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org >
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> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: Re: [gmx-users] Energy profile with umbrella sampling
> >From: "pim lists" < pimlists at googlemail.com>
> >>We are using umbrella sampling to observe a hydrogen transfer. And
> >>like to analyze our results by graphing the energy against the reaction
> >>coordinates, in order to see the energy profile for the transition
> >>Does the force constant from the umbrella sampling affect the output of
> >>g_energy? Are there any special steps that should be taken in order to
> >>Thank you for your time and assistance
> >>Robert Fiske
> >According to src/mdlib/pull.c the umbrella forces*displacement are added
> >the virial. Therefore I'd say you see back effects in the virial/pressure
> >output of g_energy.
> >The umbrella potential energy is apparently not written away anywhere,
> >you'll have to recalculate it from the displacement-from-the-mean written
> >your pull.pdo output file, and add that energy yourself to the total
> Indeed it does not seem to be added to the total energy,
> this should be stated in the manual.
> But anyhow, in most cases you do not want this contribution to the energy,
> as you would like to have the energy of the original system.
> The only thing that you need to correct for is that the sampling
> is biased by the umbrella potential, which you can recalculate from
> the displacement and the force constant.
Sorry, I must have been sleeping! In any case, you state you want an energy
profile for the transition state. Interaction energies you can get correctly
from the g_energy file, but I guess you want free energies. How could you
retrieve those? Boltzmann inversion of the distance distribution of your
coordinate + the correction of the umbrella potential?
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