From: "pim schravendijk" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
<gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Energy profile with umbrella sampling
Date: Wed, 12 Jul 2006 14:30:04 +0200
On 7/11/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] >
wrote:
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From: "Berk Hess" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Energy profile with umbrella sampling
>From: "pim lists" < [EMAIL PROTECTED]>
>>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.
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.
Berk.
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?
greetings, Pim
Actually we intend to get the activation energy of the transition state. I
was plotting the potential energy of the system obtained from g_energy
against the reaction coordinate. So based on the responses in the mailing
list, it seems quite straightforward as we do not need to bother about the
biasing potential as they are not reflected in the g_energy. Am I right?
Thanks for all your help
fiske
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