COSMO-SMD Initialization (regarding solvent accessible surface area)

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Forum Vet

3:28:31 PM PST - Fri, Jan 8th 2016
Tom Thanks for spotting this. The Solvation contribution was getting an extra E_dispersion bit. Please apply the patch http://nwchemgit.github.io/images/Solvdisp.patch.gz

Forum Vet

11:37:40 PM PST - Fri, Jan 8th 2016

Dear Edoapra

 I have applied the patch in the $NWCHEM_TOP with the following information

patching file src/nwdft/scf_dft/dft_scf.F
Hunk #1 succeeded at 1731 with fuzz 2 (offset -68 lines),

but only have got the negligible changes of energies, i.e.,

G(DFT+SMD+D2) = -248.2995362360 (patched)
G(DFT+SMD+D2)= -248.2995362369 (not patched)

G(DFT+SMD)= -248.2873891780(patched)
G(DFT+SMD)= -248.2873891789(not patched).

Forum Regular

5:15:13 PM PST - Sat, Jan 9th 2016
Hi Xiongyan, The patch addressed the dispersion correction (if requested) that was being over counted. Have you requested dispersion in your input ? Best, -Niri niri.govind@pnnl.gov

Forum Vet

7:19:32 PM PST - Sat, Jan 9th 2016

Dear Dr. Niri
Sure.
The output is like the following
DFT+SMD (PATCHED)

Total DFT energy =     -248.287389178020

     One electron energy =     -742.074418869647

          Coulomb energy =      323.492610338269

   Exchange-Corr. energy =      -35.884148630660

Nuclear repulsion energy =      205.894993671704

Numeric. integr. density =       42.000004737663

                               COSMO-SMD solvation results

                               ---------------------------

Reference for the SMD model:

Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2009, 113, 6378

            internal energy in gas <Psi(g)|H|Psi(g)> =      -248.2808746146

        internal energy in solvent <Psi(s)|H|Psi(s)> =      -248.2790851650

                              delta internal energy  =         0.0017894495 (    1.12 kcal/mol)

  total free energy in solvent <Psi(s)|H+V/2|Psi(s)> =      -248.2896667260

polarization energy contribution <Psi(s)|V/2|Psi(s)> =        -0.0105815609 (   -6.64 kcal/mol)

   total free energy in solvent including G(SMD-CDS) =      -248.2873891780

                      G(SMD-CDS) energy contribution =         0.0022775480 (    1.43 kcal/mol)

    1 M fixed-concentration free energy of solvation =        -0.0065145635 (   -4.09 kcal/mol)

DFT+SMD+D2( PATCHED)
Total DFT energy = -248.293462706986

     One electron energy =     -742.074418869647

          Coulomb energy =      323.492610338269

   Exchange-Corr. energy =      -35.884148630660

Nuclear repulsion energy =      205.894993671704

   Dispersion correction =       -0.006073528966

Numeric. integr. density =       42.000004737663

                               COSMO-SMD solvation results

                               ---------------------------

Reference for the SMD model:

Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2009, 113, 6378

            internal energy in gas <Psi(g)|H|Psi(g)> =      -248.2930216725

        internal energy in solvent <Psi(s)|H|Psi(s)> =      -248.2912322230

                              delta internal energy  =         0.0017894495 (    1.12 kcal/mol)

  total free energy in solvent <Psi(s)|H+V/2|Psi(s)> =      -248.3018137839

polarization energy contribution <Psi(s)|V/2|Psi(s)> =        -0.0105815609 (   -6.64 kcal/mol)

   total free energy in solvent including G(SMD-CDS) =      -248.2995362360

                      G(SMD-CDS) energy contribution =         0.0022775480 (    1.43 kcal/mol)

    1 M fixed-concentration free energy of solvation =        -0.0065145635 (   -4.09 kcal/mol)

Very Best Regards!

Forum Vet

7:26:46 PM PST - Sat, Jan 9th 2016

DFT+SMD (NOT PATCHED)

        Total DFT energy =     -248.287389178862

     One electron energy =     -742.074418840412

          Coulomb energy =      323.492610306750

   Exchange-Corr. energy =      -35.884148628192

Nuclear repulsion energy =      205.894993671704

Numeric. integr. density =       42.000004739972

    

                               COSMO-SMD solvation results

                               ---------------------------

Reference for the SMD model:

Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2009, 113, 6378

            internal energy in gas <Psi(g)|H|Psi(g)> =      -248.2808746155

        internal energy in solvent <Psi(s)|H|Psi(s)> =      -248.2790851664

                              delta internal energy  =         0.0017894490 (    1.12 kcal/mol)

  total free energy in solvent <Psi(s)|H+V/2|Psi(s)> =      -248.2896667268

polarization energy contribution <Psi(s)|V/2|Psi(s)> =        -0.0105815604 (   -6.64 kcal/mol)

   total free energy in solvent including G(SMD-CDS) =      -248.2873891789

                      G(SMD-CDS) energy contribution =         0.0022775480 (    1.43 kcal/mol)

    1 M fixed-concentration free energy of solvation =        -0.0065145634 (   -4.09 kcal/mol)

DFT+SMD+D2(NOT PATCHED)

Total DFT energy =     -248.293462707908

     One electron energy =     -742.074418829356

          Coulomb energy =      323.492610294997

   Exchange-Corr. energy =      -35.884148627163

Nuclear repulsion energy =      205.894993671704

   Dispersion correction =       -0.006073528966

Numeric. integr. density =       42.000004740107

                               COSMO-SMD solvation results

                               ---------------------------

Reference for the SMD model:

Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2009, 113, 6378

            internal energy in gas <Psi(g)|H|Psi(g)> =      -248.2930216735

        internal energy in solvent <Psi(s)|H|Psi(s)> =      -248.2912322243

                              delta internal energy  =         0.0017894491 (    1.12 kcal/mol)

  total free energy in solvent <Psi(s)|H+V/2|Psi(s)> =      -248.3018137848

polarization energy contribution <Psi(s)|V/2|Psi(s)> =        -0.0105815605 (   -6.64 kcal/mol)

   total free energy in solvent including G(SMD-CDS) =      -248.2995362369

                      G(SMD-CDS) energy contribution =         0.0022775480 (    1.43 kcal/mol)

    1 M fixed-concentration free energy of solvation =        -0.0065145634 (   -4.09 kcal/mol)

Very Best Regards!

Clicked A Few Times

5:24:26 PM PDT - Thu, Sep 1st 2016
Is this patch included with the patches on the download page? Is this needed to use SMD? http://nwchemgit.github.io/index.php/Download

Forum Vet

10:35:55 AM PDT - Fri, Sep 2nd 2016
It has not been included in the list of patches since it has not been fully vetted yet. Quote:Jdmoore2004 Sep 1st 4:24 pm Is this patch included with the patches on the download page? Is this needed to use SMD? http://nwchemgit.github.io/index.php/Download

Forum Vet

5:06:59 AM PST - Thu, Feb 2nd 2017

After applying all the patches except the two for the installations under other operating systems, the py output of the last step initialization becomes:

        internal energy in solvent   ... =      -248.3034894293

...

The calculation is based on the input provided here. Has it been changed?

Forum Vet

8:59:55 AM PST - Thu, Feb 2nd 2017

If only the patch for mac is applied, the results are...

        internal energy in solvent ... =      -248.3034894307

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