[gmx-users] Energy profile with umbrella sampling

Robert fiske rfiske_ at hotmail.com
Wed Jul 12 17:32:50 CEST 2006

>From: "pim schravendijk" <pimlists at googlemail.com>
>Reply-To: pimlists at gmail.com,Discussion list for GROMACS users 
><gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Energy profile with umbrella sampling
>Date: Wed, 12 Jul 2006 14:30:04 +0200
>On 7/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org >
>>Send gmx-users mailing list submissions to
>>          gmx-users at gromacs.org
>>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
>> >>this?
>> >>
>> >>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 
>> >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 
>> >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.
>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 
>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


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