On 7/10/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:
From: "Robert fiske" <[EMAIL PROTECTED] >
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
this?
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.
Greetings, Pim
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