[gmx-users] Energy profile with umbrella sampling
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Tue Jul 11 07:48:09 CEST 2006
On 7/10/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> From: "Robert fiske" <rfiske_ at hotmail.com>
> Subject: [gmx-users] Energy profile with umbrella sampling
> We are using umbrella sampling to observe a hydrogen transfer. And would
> like to analyze our results by graphing the energy against the reaction
> coordinates, in order to see the energy profile for the transition state.
> 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 do
> Thank you for your time and assistance
> Robert Fiske
According to src/mdlib/pull.c the umbrella forces*displacement are added to
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 in
your pull.pdo output file, and add that energy yourself to the total energy.
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