From: "pim lists" <[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: Tue, 11 Jul 2006 07:48:09 +0200
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.
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.
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