COSMO-SMD Initialization (regarding solvent accessible surface area)

Clicked A Few Times

10:07:06 AM PST - Mon, Dec 28th 2015

Hello,

I am using SMD solvation on a CdTe cluster model (input selections are provided below) and am getting odd results regarding the G(SMD-CDS) energy contribution. On a clean CdTe cluster model, after the cosmo initialization section NWCHEM reports: G(SMD-CDS) = 7.190 kcal/mol and a SMS-CDS SASA = 55.418 (Input and Output #1 below), whereas if I have an adsorbed hydrogen atom on the same CdTe cluster model nwchem reports: G(SMD-CDS) = 0.000 kcal/mol and SMD-CDS SASA = 0.000 ang^2 (Input and Output #2 below). In the second case, I would expect SMD-CDS SASA (and the corresponding CDS energy contribution) to be non-zero given the similarity to the geometry employed in the first case. Could anyone help me understand why I am getting values of 0.000?

Thanks in advance,
Tom

Input #1:

start "CdTe"
memory 4000 Mb

geometry noautoz

H1                   -1.79253420    -8.58929717    -1.75764609 charge 1.5

H1                    0.62359575    -9.68359177     1.76906492 charge 1.5

H1                    2.88179988    -8.28778835    -1.75733531 charge 1.5

H1                    8.33542745     2.74270851    -1.75660404 charge 1.5

H1                   -8.69679715     4.29916838     1.76771176 charge 1.5

H1                   -6.54114935     5.84744645    -1.75820071 charge 1.5

H1                    5.73643514     6.63986483    -1.75641179 charge 1.5

H1                    8.07237021     5.38170371     1.76951997 charge 1.5

H1                   -8.62248184     1.64242566    -1.75420551 charge 1.5

H2                   -5.68704512    -6.61020021    -1.50237666 charge 0.5

H2                   -4.31353070    -5.68356312    -3.90375747 charge 0.5

H2                    5.00989173    -5.08224574    -3.90413763 charge 0.5

H2                    0.34817411    -5.38290614    -3.87144755 charge 0.5

H2                    6.49018134    -5.82416961    -1.50110954 charge 0.5

H2                   -6.90597350    -1.79586283    -3.90331241 charge 0.5

H2                   -8.28878582    -2.70706910    -1.50243461 charge 0.5

H2                    2.41765728    -1.19440769    -3.90269553 charge 0.5

H2                   -0.17278133     2.69162039    -3.90300215 charge 0.5

H2                   -4.83449968     2.39095948    -3.87081106 charge 0.5

H2                   -2.24308513    -1.49562491    -3.90400427 charge 0.5

H2                    8.56880507    -1.62003953    -1.50085640 charge 0.5

H2                    4.48892220     2.99227668    -3.86869324 charge 0.5

H2                    7.08054637    -0.89416926    -3.90288738 charge 0.5

H2                   -0.46201485     7.14916943     1.79274252 charge 0.5

H2                   -2.76487856     6.57924938    -3.90256003 charge 0.5

H2                   -2.88093598     8.23444474    -1.50121972 charge 0.5

H2                    6.42274467    -3.17638343     1.79355763 charge 0.5

H2                    1.80038850     8.53308269    -1.50215559 charge 0.5

H2                    1.89787214     6.87969593    -3.90399890 charge 0.5

H2                   -5.96372715    -3.97543323     1.79249501 charge 0.5

Cd                   -1.92309071    -6.84994572    -1.14912003

Cd                    2.78841226    -6.54538404    -1.14976757

Cd                   -1.83772534    -4.27067100     1.53420074

Cd                    0.50378575    -7.80067193     1.63900756

Cd                    2.36990564    -3.99945102     1.53339230

Cd                   -4.46649284    -2.97935249    -1.17201824

Cd                   -7.06379121     0.85665246    -1.14859236

Cd                   -2.37699625     1.17513033    -1.15984818

Cd                   -7.00498473     3.46359896     1.63755684

Cd                    0.17062142    -2.64500936    -1.15968290

Cd                   -4.64749369    -0.05544230     1.53370218

Cd                    4.81410015    -2.37917044    -1.17191515

Cd                    2.20562418     1.47085427    -1.15881492

Cd                   -2.77976745     3.72492868     1.53326461

Cd                    6.89469647     1.75980268    -1.14630933

Cd                    2.27652012     4.05189514     1.53473938

Cd                    4.61650778     0.54238791     1.53422665

Cd                    6.50101475     4.33456140     1.64000910

Cd                   -4.96914219     5.09092506    -1.14956936

Cd                   -0.34607553     5.35918101    -1.17176903

Cd                    4.27424650     5.68864051    -1.14698944

Te                   -2.13733786    -7.01561718     1.68330058

Te                   -4.30350670    -5.66021492    -2.12483856

Te                    3.02182962    -6.68257723     1.68291100

Te                    0.34677775    -5.37006471    -2.06373874

Te                    4.99660737    -5.05934947    -2.12489649

Te                   -6.87861876    -1.79744088    -2.12460033

Te                   -7.29635485     0.72385828     1.68417000

Te                   -4.44015729    -2.96112363     1.66745286

Te                    2.41519477    -1.19358188    -2.13154061

Te                   -2.11943569     1.04724002     1.66605338

Te                   -2.24129196    -1.49407411    -2.13255858

Te                    1.96768891     1.31108834     1.66710745

Te                   -4.82542064     2.38485179    -2.06317783

Te                    4.78213244    -2.36585839     1.66765661

Te                   -0.17368693     2.68871227    -2.13162044

Te                    0.15175184    -2.36042211     1.66647278

Te                    7.14364266     1.65537162     1.68580106

Te                    7.05439855    -0.89654157    -2.12360734

Te                    4.47794115     2.98592428    -2.06097300

Te                   -2.74926151     6.56038189    -2.12347509

Te                   -0.34427436     5.32325374     1.66778582

Te                   -5.00545069     5.35883773     1.68299528

Te                    1.88406299     6.85679987    -2.12476666

Te                    4.27482702     5.95765404     1.68544347

end

constraints

 fix atom 1:30

end

charge 0

basis "ao basis"

 * library 6-31G** except Cd Te

 Cd library "Stuttgart RSC 1997 ECP"

 Te library "Stuttgart RLC ECP"

end

basis "cd basis"

 * library "Ahlrichs Coulomb Fitting"

end

ecp

 Cd library "Stuttgart RSC 1997 ECP"

 Te library "Stuttgart RLC ECP"

end

driver

 xyz output

 maxiter 200

end

dft

 iterations 200

 xc b3lyp

 disp vdw 2

 direct

end

cosmo

 do_cosmo_smd true

 solvent water

 do_gasphase false

end

task dft optimize

Output #1:

...... end of -cosmo- initialization ......

G(SMD-CDS) energy (kcal/mol)  =     7.190

SMD-CDS SASA (angstrom**2)    =    55.418

Input #2:

start "GaP111"

memory 4000 Mb

geometry noautoz

H1                    5.59219903     6.77947913    -1.75129237 charge 1.5

H1                    3.95626664     8.87397246     1.77169032 charge 1.5

H1                    1.31285496     8.68409788    -1.75773952 charge 1.5

H1                   -8.64079336     1.45034625    -1.76470281 charge 1.5

H1                    5.71365542    -7.83862760     1.78515175 charge 1.5

H1                    3.09008260    -8.21076468    -1.74423068 charge 1.5

H1                   -8.15021874    -3.20845549    -1.76045484 charge 1.5

H1                   -9.63896044    -1.00645844     1.76193638 charge 1.5

H1                    6.88658600    -5.45403075    -1.73703023 charge 1.5

H2                    8.12096396     3.21805987    -1.49016892 charge 0.5

H2                    6.47742799     3.03371307    -3.89348258 charge 0.5

H2                   -2.05826599     6.83313184    -3.90737968 charge 0.5

H2                    2.20949171     4.93320190    -3.86793053 charge 0.5

H2                   -3.02751139     8.17951730    -1.50691773 charge 0.5

H2                    6.96684741    -1.61305009    -3.88924288 charge 0.5

H2                    8.61155857    -1.44678510    -1.48592311 charge 0.5

H2                   -1.56905250     2.18591135    -3.90213676 charge 0.5

H2                   -1.08038413    -2.45887024    -3.89839738 charge 0.5

H2                    3.18757870    -4.35834006    -3.85944844 charge 0.5

H2                    2.69819367     0.28729591    -3.89669082 charge 0.5

H2                   -6.82107449     5.42200839    -1.50961706 charge 0.5

H2                   -5.34832238    -0.55937957    -3.87084633 charge 0.5

H2                   -5.83771060     4.08625957    -3.90908570 charge 0.5

H2                   -2.90245385    -6.53630778     1.79805701 charge 0.5

H2                   -0.59096430    -7.10563249    -3.89415667 charge 0.5

H2                   -1.26045647    -8.62355251    -1.49243219 charge 0.5

H2                   -4.20209965     5.80597744     1.78825846 charge 0.5

H2                   -5.54449554    -6.71352699    -1.50037822 charge 0.5

H2                   -4.85982687    -5.20574214    -3.90210539 charge 0.5

H2                    7.13756881     0.75887109     1.80546430 charge 0.5

Cd                    4.89733876     5.18226392    -1.14830336

Cd                    0.58165091     7.10659610    -1.15065536

Cd                    3.64090676     2.99643277     1.53173528

Cd                    3.17570117     7.16051346     1.63664155

Cd                   -0.30293522     4.76909426     1.48772985

Cd                    5.33796135     0.56904956    -1.18254196

Cd                    5.86354326    -4.04225410    -1.13469655

Cd                    1.55563614    -2.21976660    -1.14207436

Cd                    4.54744360    -6.35277994     1.65211884

Cd                    1.09839994     2.41997288    -1.17294219

Cd                    4.22307288    -2.01371877     1.52870155

Cd                   -3.15209102     4.34736530    -1.17347712

Cd                   -2.62262803    -0.27444372    -1.16587719

Cd                    0.64839967    -4.76360713     1.14061379

Cd                   -6.90838626     1.64724286    -1.15791632

Cd                   -3.92586579    -2.51383145     1.52830758

Cd                   -4.34230851     1.64990803     1.52765541

Cd                   -7.77196779    -0.79127710     1.63154216

Cd                    2.04259194    -6.86709630    -1.09926017

Cd                   -2.19586282    -4.90723835    -1.11720413

Cd                   -6.41919629    -3.05307646    -1.14355447

Te                    5.18288399     5.27530875     1.68549337

Te                    6.45262035     3.01983235    -2.11533897

Te                    0.43816738     7.43047580     1.67511932

Te                    2.19957237     4.92519961    -2.05914414

Te                   -2.06154234     6.80400048    -2.12640295

Te                    6.93749031    -1.60084051    -2.10723120 

Te                    6.07805815    -4.04446562     1.69998628 

Te                    5.32748999     0.63058749     1.66874990 

Te                   -1.56882830     2.18658856    -2.12950725 

Te                    1.46163028    -1.76276665     1.69201556 

Te                    2.67227771     0.24741647    -2.11600672 

Te                   -2.34575058    -0.24423355     1.66371016 

Te                    3.17965729    -4.39039356    -2.04850011 

Te                   -3.15253066     4.31971263     1.66866531 

Te                   -1.09547280    -2.47204092    -2.11944886 

Te                    0.97748052     2.29707816     1.67077743 

Te                   -7.08853676     1.87822297     1.67473792 

Te                   -5.81847598     4.07613221    -2.13185906 

Te                   -5.33922059    -0.56224569    -2.06238808 

Te                   -0.60690565    -7.07036227    -2.10614102 

Te                   -2.23752662    -4.84765807     1.72346758 

Te                    1.96295260    -7.24762679     1.71979865 

Te                   -4.84532947    -5.19045147    -2.12461416 

Te                   -6.57688555    -3.26513838     1.68804520 

H                     1.49447312    -0.00669412     1.68893084

end



constraints          

 fix atom 1:30       

end                  



charge 0             



basis "ao basis"     

 * library 6-31G** except Cd Te

 Cd library "Stuttgart RSC 1997 ECP" 

 Te library "Stuttgart RLC ECP"

end                   



basis "cd basis"     

 * library "Ahlrichs Coulomb Fitting"

end                   



ecp                   

 Cd library "Stuttgart RSC 1997 ECP" 

 Te library "Stuttgart RLC ECP"

end                  



driver                

 xyz output          

 maxiter 200         

end                  



dft                   

 iterations 200      

 xc b3lyp            

 disp vdw 2           

 direct               

 mult 2

end

cosmo

 do_cosmo_smd true

 solvent water

 do_gasphase false

end

task dft optimize

Output #2:

...... end of -cosmo- initialization ......

G(SMD-CDS) energy (kcal/mol)  =     0.000

SMD-CDS SASA (angstrom**2)    =     0.000

Forum Vet

4:13:05 PM PST - Mon, Dec 28th 2015
Tom What version of NWChem have you been using?

Clicked A Few Times

8:23:37 AM PST - Tue, Dec 29th 2015

I am using NWCHEM 6.6, with the recent Cosmo_meminit.patch.gz? patch installed. I've also managed to reproduce this behavior on a much simpler system, described below.

Thanks for your help,
Tom

For a pyridine molecule, nwchem reports:

G(SMD-CDS) energy (kcal/mol)  =    -7.504

SMD-CDS SASA (angstrom**2)    =    47.784

Whereas for a protonated pyridinium cation, nwchem reports:

 G(SMD-CDS) energy (kcal/mol)  =     0.000

 SMD-CDS SASA (angstrom**2)    =     0.000

Pyridine Input:

start "Molecule"

geometry

 C   -2.94367050510978      0.16884544962405     -3.27053004581723

 C   -1.56546789896111      0.28217918078066     -3.07056718320758

 C   -1.76551717814984     -0.13849758614096     -0.82589177078278

 C   -3.15324089080832     -0.27119663157549     -0.91943261168897

 C   -3.75538730016283     -0.11418293383664     -2.17050136671328

 H   -4.83117580035328     -0.21237114106753     -2.28787566294990

 H   -3.73961151467092     -0.49760106763379     -0.03462089128199

 H   -1.26892849569045     -0.26076648863257      0.13541583294285

 H   -0.91003461192482      0.50649416950745     -3.91029092683048

 H   -3.36626519586858      0.30388487907903     -4.26128038677812

 N   -0.97036181919824      0.13331228329784     -1.87461353514546

end

charge 0

basis "ao basis"

 * library 6-31G**

end

basis "cd basis"

 * library "Ahlrichs Coulomb Fitting"

end

driver

 xyz output

end

dft

 xc b3lyp

 disp vdw 2

 direct

end

cosmo

 do_cosmo_smd true

 solvent water

 do_gasphase false

end

task dft optimize

Pyridinium Input:

start "Molecule"

geometry

C    5.3646204000000    5.0679520000000    2.7827618000000

C    6.6932701000000    5.3657455000000    2.9239084000000

C    6.4615866000000    5.2721020000000    5.3394707000000

C    5.1324011000000    4.9736797000000    5.2035036000000

C    4.5330798000000    4.8541302000000    3.9179750000000

H    3.4798338000000    4.6099010000000    3.8054147000000

H    4.5439928000000    4.8287323000000    6.1091422000000

H    6.9667152000000    5.3746464000000    6.2965872000000

H    7.3686724000000    5.5428444000000    2.0907617000000

H    4.9578527000000    5.0001401000000    1.7742045000000

H    8.2284232000000    5.6987981000000    4.3052616000000

N    7.2538519000000    5.4568283000000    4.2019084000000

end

charge 1

basis "ao basis"

 * library 6-31G**

end

basis "cd basis"

 * library "Ahlrichs Coulomb Fitting"

end

driver

 xyz output

end

dft

 xc b3lyp

 disp vdw 2

 direct

end

cosmo

 do_cosmo_smd true

 solvent water

 do_gasphase false

end

task dft optimize

Forum Vet

11:27:14 AM PST - Tue, Dec 29th 2015
Could you please upload the output files to a website of your choice? I believe I am not getting the same results you are

Clicked A Few Times

12:12:02 PM PST - Tue, Dec 29th 2015
I have uploaded output files for the pyridine and pyridinium examples here: https://github.com/tsenf/COSMO_SMD Thanks, Tom

Forum Vet

2:57:53 PM PST - Tue, Dec 29th 2015
Tom Your SMD results are very different from what I am observing. Could you please 1) Run the QA tests PhoWat_SMD_HF and CH3OH2pWat_SMD_M062X 2) Provide details about the software environment used in the NWChem installation? Thanks

Forum Vet

9:27:59 PM PST - Tue, Dec 29th 2015
Even without the patch installed, there are no such cosmo initialization problems you described existing for your CdTe with an absorbed hydrogen atom and protonated pyridinium cation calculations, and the latter one converges at the 6th step, which takes 226.0 seconds for a 3-core run.

Clicked A Few Times

9:48:24 AM PST - Wed, Dec 30th 2015

Edoapra,

1) I have run the QA test cases.

For the PhoWat_SMD_HF case, I still get:

G(SMD-CDS) energy (kcal/mol)  =     0.000

SMD-CDS SASA (angstrom**2)    =     0.000

Whereas for the CH3OH2pWat_SMD_M062X case, I get the expected:

G(SMD-CDS) energy (kcal/mol)  =     3.326

SMD-CDS SASA (angstrom**2)    =    90.615

I have uploaded the complete output files here: https://github.com/tsenf/nwchem_SMD_QA

2) Our NWCHEM installation, running on a Springdale Linux OS, uses the following modules:

intel/16.0/64/16.0.0.109

intel-mkl/11.3.0/0/64

intel-mpi/intel/5.0.3.048/64

Are there any other specific details regarding our software environment that would help troubleshoot this issue?

Thanks for your help,
Tom

Forum Regular

10:48:13 AM PST - Wed, Dec 30th 2015
Hi Tom, Do you have access to the Intel 14 or 15 compilers ? If so, can you try compiling with these ? Best, -Niri niri.govind@pnnl.gov

Forum Regular

10:56:58 AM PST - Wed, Dec 30th 2015
Hi Tom, To add to my previous message. I am able to reproduce our baseline results (Pho, CH3OH cases). Best, -Niri niri.govind@pnnl.govi

Forum Vet

12:12:28 PM PST - Wed, Dec 30th 2015
Quote:Tsenf Dec 30th 8:48 am Our NWCHEM installation, running on a Springdale Linux OS, uses the following modules: intel/16.0/64/16.0.0.109 intel-mkl/11.3.0/0/64 intel-mpi/intel/5.0.3.048/64 Are there any other specific details regarding our software environment that would help troubleshoot this issue? Tom 1) Could you please provide as many details as possible about your installation, i.e. the full list of env. variables settings? 2) Could you try to recompile following this recipe i) unset all the BLASOPT, BLAS_LIB, ... env. variables where you have used MKL libraries ii) set USE_INTERNALBLAS=y iii) cd $NWCHEM_TOP//src/solvation iv) make clean; make FC=ifort FOPTIMIZE="-O0 -g" FDEBUG="-O0 -g" v) cd $NWCHEM_TOP//src; make FC=ifort link

Clicked A Few Times

3:35:49 PM PST - Mon, Jan 4th 2016
Hello Edoapra and Niri, We are currently recompiling nwchem using an Intel 14 compiler, and will post the QA results here when finished. Concerning the env. variables, is there a way to determine the env var settings that were used in our previous installation? Thanks, Tom

Forum Regular

5:38:04 PM PST - Mon, Jan 4th 2016
Hi Tom, Thanks for the update. The GA related compilation variables will be in config.log file (/src/tools/build). For all the NWChem settings, you should have a log of all the environment settings before you started the compilation. Please also try Edo's suggestion. That might help pin this down further. Best, -Niri

Forum Regular

6:47:18 AM PST - Tue, Jan 5th 2016
Hi Tom, Please also try compiling with the Intel 15 compiler if possible. As I mentioned earlier, turning on the flags that Edo suggested will help pin this down further if there is a subtle issue with the code. Thanks. Best, -Niri

Clicked A Few Times

11:25:56 AM PST - Fri, Jan 8th 2016

Dear Niri,

We have re-compiled with Intel 14, and now nwchem reproduces the QA test case SMD results. I have placed the config.log files for both our Intel 16 and Intel 14 installation here: https://github.com/tsenf/nwchem_SMD_compiler
Hopefully this will help you pin point the issue. We are also looking into compiling with Intel 15, with the debugging option turned on as suggested by Edo.

I have a few questions regarding how dispersion energies are reported in the final SMD results. When comparing DFT runs (outputs below) on a Py molecule with D2 dispersion turned on and solvation turned off, the difference in the reported "Total DFT energy" equals the dispersion correction as expected. When solvation is turned on, the difference in "Total DFT energy" equals the dispersion correction, however, when comparing the "total free energy in solvent" the energy difference equals twice the dispersion correction. Am I double counting the dispersion energy somewhere?

I have placed the input files for the following results here: https://github.com/tsenf/Py_Dispersion_SMD

DFT:

Total DFT energy =     -248.280874615300

DFT+D2:

Total DFT energy =     -248.286948144340

....

   Dispersion correction =       -0.006073528966

E(DFT+D2) - E(DFT) = E(Dispersion), as expected.

DFT+SMD:

Total DFT energy =     -248.287389181435

.....

total free energy in solvent including G(SMD-CDS) =      -248.2873891814

DFT+SMD+D2:

Total DFT energy =     -248.293462707063

.......

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

.......

Dispersion correction =       -0.006073528966

E(DFT+SMD+D2) - E(DFT+SMD) = E(Dispersion), as expected. G(DFT+SMD+D2) - G(DFT+SMD) = 2*E(Dispersion), unexpected factor of 2

Any help interpreting these results would be greatly appreciated.

Thanks and Best Regards,
Tom

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