[gmx-users] Problem with binding energy

[Billy Williams-Noonan]

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
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052