[gmx-users] Problem with binding energy

[Billy Williams-Noonan]

Apologies those were negative values.

On 18 August 2016 at 22:21, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> 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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>>
>>
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>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
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> *LinkedIn Profile
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> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>


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

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**|*   +61420 382 557

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