[gmx-users] Problem with binding energy

[Justin Lemkul]

On 8/18/16 9:37 AM, Ben Tam wrote:
> 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.
>

What happens if you just use energygrps in your single-point calculation, rather 
than trying to split your groups apart?  My guess is you're probably getting 
periodic interactions in the MD single-point energy that are not happening in 
the QM binding energies.  Or you could try turning PBC off.  If it's just a 
single-point interaction energy, there's no real need to take the "QM approach" 
and split the coordinates to re-evaluate the energy.

-Justin

>
> 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
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>> Gromacs - Gromacs<http://www.gromacs.org/>
>> www.gromacs.org<http://www.gromacs.org>
>> The development of Gromacs would not have been possible without generous funding support from the European Research Council, the Swedish Research Council, the Swedish ...
>>
>>
>>
>>> 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
>> --
>> 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.
>>
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> 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.
>

-- 
==================================================

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

==================================================