COSMO-SMD Initialization (regarding solvent accessible surface area)

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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

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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
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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

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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

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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

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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

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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

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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

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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


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