COSMO-SMD Initialization (regarding solvent accessible surface area)

From NWChem

Viewed 4450 times, With a total of 23 Posts
Jump to: navigation, search
Forum >> NWChem's corner >> NWChem functionality

Jump to page 1Prev 16
Forum Vet
Threads 8
Posts 1371
2:28:31 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://www.nwchem-sw.org/images/Solvdisp.patch.gz

Gets Around
Threads 34
Posts 146
10:37:40 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).
Edited On 7:25:29 AM PST - Thu, Jan 14th 2016 by Xiongyan21

  • Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
    Profile
    Send PM
Forum Regular
Threads 4
Posts 190
4:15:13 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

Gets Around
Threads 34
Posts 146
6:19:32 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!
Edited On 7:15:37 AM PST - Thu, Jan 14th 2016 by Xiongyan21

Gets Around
Threads 34
Posts 146
6:26:46 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!
Edited On 7:10:06 PM PST - Sat, Jan 9th 2016 by Xiongyan21

Clicked A Few Times
Threads 0
Posts 7
4:24:26 PM PDT - Thu, Sep 1st 2016
Is this patch included with the patches on the download page?

Is this needed to use SMD?

http://www.nwchem-sw.org/index.php/Download

Forum Vet
Threads 8
Posts 1371
9:35:55 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://www.nwchem-sw.org/index.php/Download

Gets Around
Threads 34
Posts 146
4:06:59 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?
Edited On 8:05:01 PM PDT - Tue, Jun 20th 2017 by Xiongyan21

Gets Around
Threads 34
Posts 146
7:59:55 AM PST - Thu, Feb 2nd 2017
If only the patch for mac is applied, the results are...
                      



        internal energy in solvent ... =      -248.3034894307
Edited On 8:10:52 PM PDT - Tue, Jun 20th 2017 by Xiongyan21


Forum >> NWChem's corner >> NWChem functionality
Jump to page 1Prev 16



Who's here now Members 0 Guests 1 Bots/Crawler 0

AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC
Retrieved from "http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1906/limit:15,15/"