COSMO-SMD Initialization (regarding solvent accessible surface area)

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 Tsenf Member Profile Send PM
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 9:07:06 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 ```

 Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop Profile Send PM
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 3:13:05 PM PST - Mon, Dec 28th 2015 Tom What version of NWChem have you been using?

 Tsenf Member Profile Send PM
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 7:23:37 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

 Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop Profile Send PM
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 10:27:14 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

 Tsenf Member Profile Send PM
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 11:12:02 AM 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

 Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop Profile Send PM
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 1:57:53 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

 Xiongyan21 Member Profile Send PM
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 8:27:59 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. Edited On 8:36:01 PM PST - Tue, Dec 29th 2015 by Xiongyan21

 Tsenf Member Profile Send PM
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 8:48:24 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

 Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop Profile Send PM
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 9:48:13 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

 Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop Profile Send PM
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 9:56:58 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

 Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop Profile Send PM
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 11:12:28 AM 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

 Tsenf Member Profile Send PM
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 2:35:49 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

 Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop Profile Send PM
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 4:38:04 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

 Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop Profile Send PM
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 5:47:18 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

 Tsenf Member Profile Send PM
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 10:25:56 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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 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

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