Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Tue, 4 Dec 2018 16:10:14 +0000

Dear Antoine,


Thank you very much for your reply.

The results make sense now. I had a look at qm2_extern_gau_module.F90 and I can see where it comes from and I can recalculate the value in the mdout file from the gaussian file.


However, I wouldn't mind some clarifications on why this is done.

Does the self-energy of the charges only corresponds to the energy for the interaction *between* the point charges or does it also include the interaction between point charges and the atom of the QM region?

I guess that it is only between charges otherwise what would be the point of doing electrostatic embedding.

So then the energy between MM point charges is included in the EEL energy, is that correct?

Are they calculated in the same manner by Amber than they are by Gaussian? The values in kcal/mol are very different so I wouldn't think so.

Then I guess if this self energy is only between the point charges, it correspond purely to the MM part so it make sense to have it calculated from the MM program based on the force field

Also, I had a look at other qm2_extern modules and it looks like for example for Orca this subtraction is not performed. Is it because Orca remove this form the total energy on its own? Or perhaps I missed it in the code.


Many thanks in advance for your help,


Eric

--
Eric Lang
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
________________________________
From: Antoine MARION <amarion.metu.edu.tr>
Sent: 04 December 2018 14:22:56
To: AMBER Mailing List
Subject: Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Dear Eric,
As far as I see from the code, you should also subtract the “Self energy of the charges” (as found in the Gaussian output) to match EXTERNESCF.
Probably to avoid double counting. (?)
EXTERNESCF = E(RwB97XD) - self_energy
Best,
Antoine
____________________________
-- Dr. Antoine MARION
Assistant Professor
Doktor Öğretim Üyesi
Department of Chemistry
Middle East Technical University
06800, Ankara, Turkey
Office: O-310
Email: amarion.metu.edu.tr <mailto:amarion.metu.edu.tr>
Phone: +90 312 210 51 44
> On 4 Dec 2018, at 14:36, Eric Lang <eric.lang.bristol.ac.uk> wrote:
>
> Dear Amber Developers and Users,
>
>
>
> I am running some single point QM/MM in Sander (compiled as Amber16+AmberTools17) using Gaussian 09.
>
> The calculations run ok, but I think something is not quite right with the extraction of the QM energy from the gaussian output file: the EXTERNESCF energy in the mdout file in kcal/mol doesn’t match the final energy (last ‘SCF Done’ line or ‘HF’ at the very end of the Gaussian file) when converted to kcal/mol using the conversion used in Amber (AU_TO_KCAL  =  6.2750946943E+02).
>
> I would think they should be the same.
>
> Am I missing something obvious in the way the calculations are done or is there a problem with the way the gaussian output files are parsed?
>
>
>
> Here is the output form Amber:
>
>
>
>                    FINAL RESULTS
>
>   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>
>      1      -5.0519E+05     1.3953E+01     1.1652E+02     CA       1579
>
>
>
> BOND    =      456.4977  ANGLE   =     1327.2559  DIHED      =     2177.6750
>
> VDWAALS =     8267.2236  EEL     =   -89612.1756  HBOND      =        0.0000
>
> 1-4 VDW =      625.9136  1-4 EEL =     7948.6914  RESTRAINT  =        0.0000
>
> EXTERNESCF =  -436379.7510
>
>
>
> And here is the final energy from Gaussian
>
>
>
> SCF Done:  E(RwB97XD) =  -3178.95512525     A.U.
>
>
>
> Which gives -1994824.4 kcal/mol and not -436379.7510 kcal/mol as found in EXTERNESCF.
>
>
>
> Many thanks in advance for your help,
>
>
>
> Eric
>
>
>
> --
>
> Eric Lang
>
> Centre for Computational Chemistry
> School of Chemistry - University of Bristol
> Bristol BS8 1TS - United Kingdom
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Dec 04 2018 - 08:30:03 PST