# [gmx-users] Problem with binding energy

Billy Williams-Noonan billy.williams-noonan at monash.edu
Thu Aug 18 14:21:47 CEST 2016

```So gromacs gives an answer of 6000 kJ/mol and some other software using the
same method yields 250 kJ/mol ?

On 18 August 2016 at 22:13, Ben Tam <btam125 at hotmail.co.uk> wrote:

> Hi Billy,
>
>
> 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.
>
> Best regards,
>
> Ben
>
> ________________________________
> 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
>
> Hi Ben,
>
>    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...
>
> Billy
>
> 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 ,
> >
> >
> > Ben
> >
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Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon