The adaptive buffered force QM/MM method in the CP2K and AMBER software packages
The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of th...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Mones, Letif [verfasserIn] |
|---|
| Format: |
Artikel |
|---|---|
| Sprache: |
Englisch |
| Erschienen: |
2015 |
|---|
| Rechteinformationen: |
Nutzungsrecht: © 2015 Wiley Periodicals, Inc. |
|---|
| Schlagwörter: |
adaptive quantum‐mechanics/molecular‐mechanics |
|---|
| Systematik: |
|
|---|
| Übergeordnetes Werk: |
Enthalten in: Journal of computational chemistry - New York, NY : Wiley, 1980, 36(2015), 9, Seite 633-648 |
|---|---|
| Übergeordnetes Werk: |
volume:36 ; year:2015 ; number:9 ; pages:633-648 |
| Links: |
|---|
| DOI / URN: |
10.1002/jcc.23839 |
|---|
| Katalog-ID: |
OLC1968337016 |
|---|
| LEADER | 01000caa a2200265 4500 | ||
|---|---|---|---|
| 001 | OLC1968337016 | ||
| 003 | DE-627 | ||
| 005 | 20220219071040.0 | ||
| 007 | tu | ||
| 008 | 160206s2015 xx ||||| 00| ||eng c | ||
| 024 | 7 | |a 10.1002/jcc.23839 |2 doi | |
| 028 | 5 | 2 | |a PQ20160617 |
| 035 | |a (DE-627)OLC1968337016 | ||
| 035 | |a (DE-599)GBVOLC1968337016 | ||
| 035 | |a (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 | ||
| 035 | |a (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 082 | 0 | 4 | |a 540 |q DNB |
| 084 | |a VA 5105 |q AVZ |2 rvk | ||
| 084 | |a 35.05 |2 bkl | ||
| 100 | 1 | |a Mones, Letif |e verfasserin |4 aut | |
| 245 | 1 | 4 | |a The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
| 264 | 1 | |c 2015 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ohne Hilfsmittel zu benutzen |b n |2 rdamedia | ||
| 338 | |a Band |b nc |2 rdacarrier | ||
| 520 | |a The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. | ||
| 540 | |a Nutzungsrecht: © 2015 Wiley Periodicals, Inc. | ||
| 650 | 4 | |a force‐mixing | |
| 650 | 4 | |a adaptive quantum‐mechanics/molecular‐mechanics | |
| 650 | 4 | |a multiscale | |
| 650 | 4 | |a quantum‐mechanics/molecular‐mechanics | |
| 650 | 4 | |a Quantum physics | |
| 650 | 4 | |a Molecular chemistry | |
| 650 | 4 | |a Software packages | |
| 650 | 4 | |a Computer simulation | |
| 650 | 4 | |a Benchmarks | |
| 650 | 4 | |a Water - chemistry | |
| 650 | 4 | |a Zinc - chemistry | |
| 650 | 4 | |a Organophosphorus Compounds - chemistry | |
| 700 | 1 | |a Jones, Andrew |4 oth | |
| 700 | 1 | |a Götz, Andreas W |4 oth | |
| 700 | 1 | |a Laino, Teodoro |4 oth | |
| 700 | 1 | |a Walker, Ross C |4 oth | |
| 700 | 1 | |a Leimkuhler, Ben |4 oth | |
| 700 | 1 | |a Csányi, Gábor |4 oth | |
| 700 | 1 | |a Bernstein, Noam |4 oth | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of computational chemistry |d New York, NY : Wiley, 1980 |g 36(2015), 9, Seite 633-648 |w (DE-627)129860301 |w (DE-600)282917-4 |w (DE-576)015169324 |x 0192-8651 |7 nnns |
| 773 | 1 | 8 | |g volume:36 |g year:2015 |g number:9 |g pages:633-648 |
| 856 | 4 | 1 | |u http://dx.doi.org/10.1002/jcc.23839 |3 Volltext |
| 856 | 4 | 2 | |u http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract |
| 856 | 4 | 2 | |u http://www.ncbi.nlm.nih.gov/pubmed/25649827 |
| 856 | 4 | 2 | |u http://search.proquest.com/docview/1659816445 |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a SYSFLAG_A | ||
| 912 | |a GBV_OLC | ||
| 912 | |a SSG-OLC-CHE | ||
| 912 | |a SSG-OLC-MAT | ||
| 912 | |a SSG-OPC-MAT | ||
| 912 | |a GBV_ILN_70 | ||
| 912 | |a GBV_ILN_4012 | ||
| 936 | r | v | |a VA 5105 |
| 936 | b | k | |a 35.05 |q AVZ |
| 951 | |a AR | ||
| 952 | |d 36 |j 2015 |e 9 |h 633-648 | ||
| author_variant |
l m lm |
|---|---|
| matchkey_str |
article:01928651:2015----::haatvbfeefremmehdnhc2adm |
| hierarchy_sort_str |
2015 |
| bklnumber |
35.05 |
| publishDate |
2015 |
| allfields |
10.1002/jcc.23839 doi PQ20160617 (DE-627)OLC1968337016 (DE-599)GBVOLC1968337016 (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso DE-627 ger DE-627 rakwb eng 540 DNB VA 5105 AVZ rvk 35.05 bkl Mones, Letif verfasserin aut The adaptive buffered force QM/MM method in the CP2K and AMBER software packages 2015 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. Nutzungsrecht: © 2015 Wiley Periodicals, Inc. force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry Jones, Andrew oth Götz, Andreas W oth Laino, Teodoro oth Walker, Ross C oth Leimkuhler, Ben oth Csányi, Gábor oth Bernstein, Noam oth Enthalten in Journal of computational chemistry New York, NY : Wiley, 1980 36(2015), 9, Seite 633-648 (DE-627)129860301 (DE-600)282917-4 (DE-576)015169324 0192-8651 nnns volume:36 year:2015 number:9 pages:633-648 http://dx.doi.org/10.1002/jcc.23839 Volltext http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract http://www.ncbi.nlm.nih.gov/pubmed/25649827 http://search.proquest.com/docview/1659816445 GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-CHE SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_70 GBV_ILN_4012 VA 5105 35.05 AVZ AR 36 2015 9 633-648 |
| spelling |
10.1002/jcc.23839 doi PQ20160617 (DE-627)OLC1968337016 (DE-599)GBVOLC1968337016 (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso DE-627 ger DE-627 rakwb eng 540 DNB VA 5105 AVZ rvk 35.05 bkl Mones, Letif verfasserin aut The adaptive buffered force QM/MM method in the CP2K and AMBER software packages 2015 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. Nutzungsrecht: © 2015 Wiley Periodicals, Inc. force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry Jones, Andrew oth Götz, Andreas W oth Laino, Teodoro oth Walker, Ross C oth Leimkuhler, Ben oth Csányi, Gábor oth Bernstein, Noam oth Enthalten in Journal of computational chemistry New York, NY : Wiley, 1980 36(2015), 9, Seite 633-648 (DE-627)129860301 (DE-600)282917-4 (DE-576)015169324 0192-8651 nnns volume:36 year:2015 number:9 pages:633-648 http://dx.doi.org/10.1002/jcc.23839 Volltext http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract http://www.ncbi.nlm.nih.gov/pubmed/25649827 http://search.proquest.com/docview/1659816445 GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-CHE SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_70 GBV_ILN_4012 VA 5105 35.05 AVZ AR 36 2015 9 633-648 |
| allfields_unstemmed |
10.1002/jcc.23839 doi PQ20160617 (DE-627)OLC1968337016 (DE-599)GBVOLC1968337016 (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso DE-627 ger DE-627 rakwb eng 540 DNB VA 5105 AVZ rvk 35.05 bkl Mones, Letif verfasserin aut The adaptive buffered force QM/MM method in the CP2K and AMBER software packages 2015 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. Nutzungsrecht: © 2015 Wiley Periodicals, Inc. force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry Jones, Andrew oth Götz, Andreas W oth Laino, Teodoro oth Walker, Ross C oth Leimkuhler, Ben oth Csányi, Gábor oth Bernstein, Noam oth Enthalten in Journal of computational chemistry New York, NY : Wiley, 1980 36(2015), 9, Seite 633-648 (DE-627)129860301 (DE-600)282917-4 (DE-576)015169324 0192-8651 nnns volume:36 year:2015 number:9 pages:633-648 http://dx.doi.org/10.1002/jcc.23839 Volltext http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract http://www.ncbi.nlm.nih.gov/pubmed/25649827 http://search.proquest.com/docview/1659816445 GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-CHE SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_70 GBV_ILN_4012 VA 5105 35.05 AVZ AR 36 2015 9 633-648 |
| allfieldsGer |
10.1002/jcc.23839 doi PQ20160617 (DE-627)OLC1968337016 (DE-599)GBVOLC1968337016 (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso DE-627 ger DE-627 rakwb eng 540 DNB VA 5105 AVZ rvk 35.05 bkl Mones, Letif verfasserin aut The adaptive buffered force QM/MM method in the CP2K and AMBER software packages 2015 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. Nutzungsrecht: © 2015 Wiley Periodicals, Inc. force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry Jones, Andrew oth Götz, Andreas W oth Laino, Teodoro oth Walker, Ross C oth Leimkuhler, Ben oth Csányi, Gábor oth Bernstein, Noam oth Enthalten in Journal of computational chemistry New York, NY : Wiley, 1980 36(2015), 9, Seite 633-648 (DE-627)129860301 (DE-600)282917-4 (DE-576)015169324 0192-8651 nnns volume:36 year:2015 number:9 pages:633-648 http://dx.doi.org/10.1002/jcc.23839 Volltext http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract http://www.ncbi.nlm.nih.gov/pubmed/25649827 http://search.proquest.com/docview/1659816445 GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-CHE SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_70 GBV_ILN_4012 VA 5105 35.05 AVZ AR 36 2015 9 633-648 |
| allfieldsSound |
10.1002/jcc.23839 doi PQ20160617 (DE-627)OLC1968337016 (DE-599)GBVOLC1968337016 (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso DE-627 ger DE-627 rakwb eng 540 DNB VA 5105 AVZ rvk 35.05 bkl Mones, Letif verfasserin aut The adaptive buffered force QM/MM method in the CP2K and AMBER software packages 2015 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. Nutzungsrecht: © 2015 Wiley Periodicals, Inc. force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry Jones, Andrew oth Götz, Andreas W oth Laino, Teodoro oth Walker, Ross C oth Leimkuhler, Ben oth Csányi, Gábor oth Bernstein, Noam oth Enthalten in Journal of computational chemistry New York, NY : Wiley, 1980 36(2015), 9, Seite 633-648 (DE-627)129860301 (DE-600)282917-4 (DE-576)015169324 0192-8651 nnns volume:36 year:2015 number:9 pages:633-648 http://dx.doi.org/10.1002/jcc.23839 Volltext http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract http://www.ncbi.nlm.nih.gov/pubmed/25649827 http://search.proquest.com/docview/1659816445 GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-CHE SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_70 GBV_ILN_4012 VA 5105 35.05 AVZ AR 36 2015 9 633-648 |
| language |
English |
| source |
Enthalten in Journal of computational chemistry 36(2015), 9, Seite 633-648 volume:36 year:2015 number:9 pages:633-648 |
| sourceStr |
Enthalten in Journal of computational chemistry 36(2015), 9, Seite 633-648 volume:36 year:2015 number:9 pages:633-648 |
| format_phy_str_mv |
Article |
| institution |
findex.gbv.de |
| topic_facet |
force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry |
| dewey-raw |
540 |
| isfreeaccess_bool |
false |
| container_title |
Journal of computational chemistry |
| authorswithroles_txt_mv |
Mones, Letif @@aut@@ Jones, Andrew @@oth@@ Götz, Andreas W @@oth@@ Laino, Teodoro @@oth@@ Walker, Ross C @@oth@@ Leimkuhler, Ben @@oth@@ Csányi, Gábor @@oth@@ Bernstein, Noam @@oth@@ |
| publishDateDaySort_date |
2015-01-01T00:00:00Z |
| hierarchy_top_id |
129860301 |
| dewey-sort |
3540 |
| id |
OLC1968337016 |
| language_de |
englisch |
| fullrecord |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a2200265 4500</leader><controlfield tag="001">OLC1968337016</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20220219071040.0</controlfield><controlfield tag="007">tu</controlfield><controlfield tag="008">160206s2015 xx ||||| 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1002/jcc.23839</subfield><subfield code="2">doi</subfield></datafield><datafield tag="028" ind1="5" ind2="2"><subfield code="a">PQ20160617</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)OLC1968337016</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)GBVOLC1968337016</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="082" ind1="0" ind2="4"><subfield code="a">540</subfield><subfield code="q">DNB</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">VA 5105</subfield><subfield code="q">AVZ</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">35.05</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Mones, Letif</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="4"><subfield code="a">The adaptive buffered force QM/MM method in the CP2K and AMBER software packages</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2015</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">ohne Hilfsmittel zu benutzen</subfield><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Band</subfield><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives.</subfield></datafield><datafield tag="540" ind1=" " ind2=" "><subfield code="a">Nutzungsrecht: © 2015 Wiley Periodicals, Inc.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">force‐mixing</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">adaptive quantum‐mechanics/molecular‐mechanics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">multiscale</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">quantum‐mechanics/molecular‐mechanics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Quantum physics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Molecular chemistry</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Software packages</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Computer simulation</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Benchmarks</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Water - chemistry</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Zinc - chemistry</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Organophosphorus Compounds - chemistry</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Jones, Andrew</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Götz, Andreas W</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Laino, Teodoro</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Walker, Ross C</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Leimkuhler, Ben</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Csányi, Gábor</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Bernstein, Noam</subfield><subfield code="4">oth</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">Journal of computational chemistry</subfield><subfield code="d">New York, NY : Wiley, 1980</subfield><subfield code="g">36(2015), 9, Seite 633-648</subfield><subfield code="w">(DE-627)129860301</subfield><subfield code="w">(DE-600)282917-4</subfield><subfield code="w">(DE-576)015169324</subfield><subfield code="x">0192-8651</subfield><subfield code="7">nnns</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:36</subfield><subfield code="g">year:2015</subfield><subfield code="g">number:9</subfield><subfield code="g">pages:633-648</subfield></datafield><datafield tag="856" ind1="4" ind2="1"><subfield code="u">http://dx.doi.org/10.1002/jcc.23839</subfield><subfield code="3">Volltext</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">http://www.ncbi.nlm.nih.gov/pubmed/25649827</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">http://search.proquest.com/docview/1659816445</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_OLC</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OLC-CHE</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OLC-MAT</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OPC-MAT</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_70</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4012</subfield></datafield><datafield tag="936" ind1="r" ind2="v"><subfield code="a">VA 5105</subfield></datafield><datafield tag="936" ind1="b" ind2="k"><subfield code="a">35.05</subfield><subfield code="q">AVZ</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">36</subfield><subfield code="j">2015</subfield><subfield code="e">9</subfield><subfield code="h">633-648</subfield></datafield></record></collection>
|
| author |
Mones, Letif |
| spellingShingle |
Mones, Letif ddc 540 rvk VA 5105 bkl 35.05 misc force‐mixing misc adaptive quantum‐mechanics/molecular‐mechanics misc multiscale misc quantum‐mechanics/molecular‐mechanics misc Quantum physics misc Molecular chemistry misc Software packages misc Computer simulation misc Benchmarks misc Water - chemistry misc Zinc - chemistry misc Organophosphorus Compounds - chemistry The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
| authorStr |
Mones, Letif |
| ppnlink_with_tag_str_mv |
@@773@@(DE-627)129860301 |
| format |
Article |
| dewey-ones |
540 - Chemistry & allied sciences |
| delete_txt_mv |
keep |
| author_role |
aut |
| collection |
OLC |
| remote_str |
false |
| illustrated |
Not Illustrated |
| issn |
0192-8651 |
| topic_title |
540 DNB VA 5105 AVZ rvk 35.05 bkl The adaptive buffered force QM/MM method in the CP2K and AMBER software packages force‐mixing adaptive quantum‐mechanics/molecular‐mechanics multiscale quantum‐mechanics/molecular‐mechanics Quantum physics Molecular chemistry Software packages Computer simulation Benchmarks Water - chemistry Zinc - chemistry Organophosphorus Compounds - chemistry |
| topic |
ddc 540 rvk VA 5105 bkl 35.05 misc force‐mixing misc adaptive quantum‐mechanics/molecular‐mechanics misc multiscale misc quantum‐mechanics/molecular‐mechanics misc Quantum physics misc Molecular chemistry misc Software packages misc Computer simulation misc Benchmarks misc Water - chemistry misc Zinc - chemistry misc Organophosphorus Compounds - chemistry |
| topic_unstemmed |
ddc 540 rvk VA 5105 bkl 35.05 misc force‐mixing misc adaptive quantum‐mechanics/molecular‐mechanics misc multiscale misc quantum‐mechanics/molecular‐mechanics misc Quantum physics misc Molecular chemistry misc Software packages misc Computer simulation misc Benchmarks misc Water - chemistry misc Zinc - chemistry misc Organophosphorus Compounds - chemistry |
| topic_browse |
ddc 540 rvk VA 5105 bkl 35.05 misc force‐mixing misc adaptive quantum‐mechanics/molecular‐mechanics misc multiscale misc quantum‐mechanics/molecular‐mechanics misc Quantum physics misc Molecular chemistry misc Software packages misc Computer simulation misc Benchmarks misc Water - chemistry misc Zinc - chemistry misc Organophosphorus Compounds - chemistry |
| format_facet |
Aufsätze Gedruckte Aufsätze |
| format_main_str_mv |
Text Zeitschrift/Artikel |
| carriertype_str_mv |
nc |
| author2_variant |
a j aj a w g aw awg t l tl r c w rc rcw b l bl g c gc n b nb |
| hierarchy_parent_title |
Journal of computational chemistry |
| hierarchy_parent_id |
129860301 |
| dewey-tens |
540 - Chemistry |
| hierarchy_top_title |
Journal of computational chemistry |
| isfreeaccess_txt |
false |
| familylinks_str_mv |
(DE-627)129860301 (DE-600)282917-4 (DE-576)015169324 |
| title |
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
| ctrlnum |
(DE-627)OLC1968337016 (DE-599)GBVOLC1968337016 (PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3 (KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso |
| title_full |
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
| author_sort |
Mones, Letif |
| journal |
Journal of computational chemistry |
| journalStr |
Journal of computational chemistry |
| lang_code |
eng |
| isOA_bool |
false |
| dewey-hundreds |
500 - Science |
| recordtype |
marc |
| publishDateSort |
2015 |
| contenttype_str_mv |
txt |
| container_start_page |
633 |
| author_browse |
Mones, Letif |
| container_volume |
36 |
| class |
540 DNB VA 5105 AVZ rvk 35.05 bkl |
| format_se |
Aufsätze |
| author-letter |
Mones, Letif |
| doi_str_mv |
10.1002/jcc.23839 |
| dewey-full |
540 |
| title_sort |
adaptive buffered force qm/mm method in the cp2k and amber software packages |
| title_auth |
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
| abstract |
The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. |
| abstractGer |
The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. |
| abstract_unstemmed |
The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives. |
| collection_details |
GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-CHE SSG-OLC-MAT SSG-OPC-MAT GBV_ILN_70 GBV_ILN_4012 |
| container_issue |
9 |
| title_short |
The adaptive buffered force QM/MM method in the CP2K and AMBER software packages |
| url |
http://dx.doi.org/10.1002/jcc.23839 http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract http://www.ncbi.nlm.nih.gov/pubmed/25649827 http://search.proquest.com/docview/1659816445 |
| remote_bool |
false |
| author2 |
Jones, Andrew Götz, Andreas W Laino, Teodoro Walker, Ross C Leimkuhler, Ben Csányi, Gábor Bernstein, Noam |
| author2Str |
Jones, Andrew Götz, Andreas W Laino, Teodoro Walker, Ross C Leimkuhler, Ben Csányi, Gábor Bernstein, Noam |
| ppnlink |
129860301 |
| mediatype_str_mv |
n |
| isOA_txt |
false |
| hochschulschrift_bool |
false |
| author2_role |
oth oth oth oth oth oth oth |
| doi_str |
10.1002/jcc.23839 |
| up_date |
2024-07-04T03:07:30.535Z |
| _version_ |
1803616204140576768 |
| fullrecord_marcxml |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a2200265 4500</leader><controlfield tag="001">OLC1968337016</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20220219071040.0</controlfield><controlfield tag="007">tu</controlfield><controlfield tag="008">160206s2015 xx ||||| 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1002/jcc.23839</subfield><subfield code="2">doi</subfield></datafield><datafield tag="028" ind1="5" ind2="2"><subfield code="a">PQ20160617</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)OLC1968337016</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)GBVOLC1968337016</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(PRQ)c2619-8098b8e05e9fd80669db2ff1674a1a259a4dedde2c03e383fab6f41ea2b735de3</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(KEY)0100255420150000036000900633adaptivebufferedforceqmmmmethodinthecp2kandamberso</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="082" ind1="0" ind2="4"><subfield code="a">540</subfield><subfield code="q">DNB</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">VA 5105</subfield><subfield code="q">AVZ</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">35.05</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Mones, Letif</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="4"><subfield code="a">The adaptive buffered force QM/MM method in the CP2K and AMBER software packages</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2015</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">ohne Hilfsmittel zu benutzen</subfield><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Band</subfield><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 Wiley Periodicals, Inc. Implementations of an adaptive method for QM/MM simulations in the CP2K and AMBER packages are presented, making it straightforward to quantum mechanically describe not only the reacting species, but also a surrounding region of solvent, because the set of quantum atoms can be changed adaptively in the simulation. Geometries and free energy profiles are compared to those of full quantum mechanical simulations to show that the method is more robust than alternatives.</subfield></datafield><datafield tag="540" ind1=" " ind2=" "><subfield code="a">Nutzungsrecht: © 2015 Wiley Periodicals, Inc.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">force‐mixing</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">adaptive quantum‐mechanics/molecular‐mechanics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">multiscale</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">quantum‐mechanics/molecular‐mechanics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Quantum physics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Molecular chemistry</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Software packages</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Computer simulation</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Benchmarks</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Water - chemistry</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Zinc - chemistry</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Organophosphorus Compounds - chemistry</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Jones, Andrew</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Götz, Andreas W</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Laino, Teodoro</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Walker, Ross C</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Leimkuhler, Ben</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Csányi, Gábor</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Bernstein, Noam</subfield><subfield code="4">oth</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">Journal of computational chemistry</subfield><subfield code="d">New York, NY : Wiley, 1980</subfield><subfield code="g">36(2015), 9, Seite 633-648</subfield><subfield code="w">(DE-627)129860301</subfield><subfield code="w">(DE-600)282917-4</subfield><subfield code="w">(DE-576)015169324</subfield><subfield code="x">0192-8651</subfield><subfield code="7">nnns</subfield></datafield><datafield tag="773" ind1="1" ind2="8"><subfield code="g">volume:36</subfield><subfield code="g">year:2015</subfield><subfield code="g">number:9</subfield><subfield code="g">pages:633-648</subfield></datafield><datafield tag="856" ind1="4" ind2="1"><subfield code="u">http://dx.doi.org/10.1002/jcc.23839</subfield><subfield code="3">Volltext</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/abstract</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">http://www.ncbi.nlm.nih.gov/pubmed/25649827</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="u">http://search.proquest.com/docview/1659816445</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_USEFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SYSFLAG_A</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_OLC</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OLC-CHE</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OLC-MAT</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">SSG-OPC-MAT</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_70</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">GBV_ILN_4012</subfield></datafield><datafield tag="936" ind1="r" ind2="v"><subfield code="a">VA 5105</subfield></datafield><datafield tag="936" ind1="b" ind2="k"><subfield code="a">35.05</subfield><subfield code="q">AVZ</subfield></datafield><datafield tag="951" ind1=" " ind2=" "><subfield code="a">AR</subfield></datafield><datafield tag="952" ind1=" " ind2=" "><subfield code="d">36</subfield><subfield code="j">2015</subfield><subfield code="e">9</subfield><subfield code="h">633-648</subfield></datafield></record></collection>
|
| score |
7.4006395 |