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COSMO-SMD Initialization (regarding solvent accessible surface area)
From NWChem
Viewed 4449 times, With a total of 23 Posts
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Posts 9
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| 9:07:06 AM PST - Mon, Dec 28th 2015 |
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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
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 8
Posts 1371
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| 3:13:05 PM PST - Mon, Dec 28th 2015 |
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Tom
What version of NWChem have you been using?
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Clicked A Few Times
Threads 2
Posts 9
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| 7:23:37 AM PST - Tue, Dec 29th 2015 |
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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
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 8
Posts 1371
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| 10:27:14 AM PST - Tue, Dec 29th 2015 |
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Could you please upload the output files to a website of your choice?
I believe I am not getting the same results you are
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Clicked A Few Times
Threads 2
Posts 9
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| 11:12:02 AM PST - Tue, Dec 29th 2015 |
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I have uploaded output files for the pyridine and pyridinium examples here: https://github.com/tsenf/COSMO_SMD
Thanks,
Tom
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Threads 8
Posts 1371
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| 1:57:53 PM PST - Tue, Dec 29th 2015 |
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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
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Gets Around
Threads 34
Posts 146
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| 8:27:59 PM PST - Tue, Dec 29th 2015 |
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| 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.
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Edited On 8:36:01 PM PST - Tue, Dec 29th 2015 by Xiongyan21
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Threads 2
Posts 9
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| 8:48:24 AM PST - Wed, Dec 30th 2015 |
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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
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 4
Posts 190
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| 9:48:13 AM PST - Wed, Dec 30th 2015 |
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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
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 4
Posts 190
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| 9:56:58 AM PST - Wed, Dec 30th 2015 |
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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
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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| 11:12:28 AM PST - Wed, Dec 30th 2015 |
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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
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Clicked A Few Times
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| 2:35:49 PM PST - Mon, Jan 4th 2016 |
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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
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 4
Posts 190
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| 4:38:04 PM PST - Mon, Jan 4th 2016 |
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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
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 4
Posts 190
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| 5:47:18 AM PST - Tue, Jan 5th 2016 |
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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
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Clicked A Few Times
Threads 2
Posts 9
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| 10:25:56 AM PST - Fri, Jan 8th 2016 |
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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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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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| 2:28:31 PM PST - Fri, Jan 8th 2016 |
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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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