Property map collective variable as a useful tool for force field correction
Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the d...
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ftdatacite:10.24435/materialscloud:yp-51 2023-05-15T17:53:44+02:00 Property map collective variable as a useful tool for force field correction Trapl, Dalibor Krupička, Martin Višňovský, Vladimir Hozzová, Jana Oľha, Jaroslav Křenek, Aleš Spiwok, Vojtěch 2021 https://dx.doi.org/10.24435/materialscloud:yp-51 https://archive.materialscloud.org/record/2021.84 en eng Materials Cloud Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode info:eu-repo/semantics/openAccess CC-BY molecular dynamics simulation molecular mechanics DFT free energy dataset Dataset 2021 ftdatacite https://doi.org/10.24435/materialscloud:yp-51 2021-11-05T12:55:41Z Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT). Simulations were carried out in Gromacs 2016.4. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory. Dataset Orca DataCite Metadata Store (German National Library of Science and Technology) Lambda ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
molecular dynamics simulation molecular mechanics DFT free energy |
spellingShingle |
molecular dynamics simulation molecular mechanics DFT free energy Trapl, Dalibor Krupička, Martin Višňovský, Vladimir Hozzová, Jana Oľha, Jaroslav Křenek, Aleš Spiwok, Vojtěch Property map collective variable as a useful tool for force field correction |
topic_facet |
molecular dynamics simulation molecular mechanics DFT free energy |
description |
Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT). Simulations were carried out in Gromacs 2016.4. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory. |
format |
Dataset |
author |
Trapl, Dalibor Krupička, Martin Višňovský, Vladimir Hozzová, Jana Oľha, Jaroslav Křenek, Aleš Spiwok, Vojtěch |
author_facet |
Trapl, Dalibor Krupička, Martin Višňovský, Vladimir Hozzová, Jana Oľha, Jaroslav Křenek, Aleš Spiwok, Vojtěch |
author_sort |
Trapl, Dalibor |
title |
Property map collective variable as a useful tool for force field correction |
title_short |
Property map collective variable as a useful tool for force field correction |
title_full |
Property map collective variable as a useful tool for force field correction |
title_fullStr |
Property map collective variable as a useful tool for force field correction |
title_full_unstemmed |
Property map collective variable as a useful tool for force field correction |
title_sort |
property map collective variable as a useful tool for force field correction |
publisher |
Materials Cloud |
publishDate |
2021 |
url |
https://dx.doi.org/10.24435/materialscloud:yp-51 https://archive.materialscloud.org/record/2021.84 |
long_lat |
ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
geographic |
Lambda |
geographic_facet |
Lambda |
genre |
Orca |
genre_facet |
Orca |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.24435/materialscloud:yp-51 |
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1766161445824757760 |