[gmx-users] Problem with binding energy
btam125 at hotmail.co.uk
Thu Aug 18 14:13:59 CEST 2016
To be more exact, the system has been energy minimised through DFT calculation. We want to compare that with MM force field by using the same co-ordinate. Henceforth we don't need an average gibbs energy but one specific frame energy calculation.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Billy Williams-Noonan <billy.williams-noonan at monash.edu>
Sent: 18 August 2016 13:07
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem with binding energy
My understanding of what you've done is that you have calculated a
binding enthalpy for the water at a specific, non-biological temperature,
and not a Gibbs free energy that you would expect from experiment...
On 18 August 2016 at 21:34, Ben Tam <btam125 at hotmail.co.uk> wrote:
> Dear all,
> I have a problem with calculation with binding energy with using gromacs.
> My calculation is the binding of solvent onto a crystal.
> The steps I took to calculate binding energy is like this:
> 1) Energy minimised my crystal system with the solvent.
> 2) Calculated the energy of the crystal-solvent system by using gmx energy
> - total energy is selected (this is done by using only time 0 energy step
> shown from energy.xvg)
> 3) I extract the co-ordinate of the solvent from the minimised system and
> calculate the energy by using gmx energy - total energy is selected (this
> is done by using only time step 0 energy shown from energy.xvg)
> 4)Extract the co-ordinate of the crystal from the minimised system and
> calculate the energy similar to the previous step.
> 5) Energy of the Crystalsolvent system - energy of the crystal - energy of
> the solvent = binding energy.
> The problem I have is, after the calculation I proposed, the binding shown
> as -6000 kJ/mol. With other software, the binding energy is calculated as
> -250 kJ/mol.
> I have triple check my molecules connectivity and the charges and the
> force field. Everything seems to be reasonable. Henceforth, what can caused
> the extremely high binding energy?
> Thanks ,
> Gromacs Users mailing list
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