[gmx-users] Problem with binding energy

[Ben Tam]

Hi Justin,


Yes I am, doing 3 single point simulation but using a very long winded way of doing single - point energy. The DFT calculation gave me -357 kJ/mol, the other software I mentioned is Forcite, which gave me around -250 kJ/mol.


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 Justin Lemkul <jalemkul at vt.edu>
Sent: 18 August 2016 13:21
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem with binding energy



On 8/18/16 8:13 AM, Ben Tam 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.
>

You're doing the single-point energy correctly, right?

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
Single-Point Energy - Gromacs<http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy>
www.gromacs.org
Computing the energy of a single configuration is an operation that is sometimes useful. The best way to do this with GROMACS is with the mdrun -rerun mechanism ...




It's not clear to me from the description whether you are or not.

The -250 kJ/mol is the interaction energy from DFT, I presume?

-Justin

> 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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--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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