Property map collective variable as a usefultool for force field correction - analysis
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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ftzenodo:oai:zenodo.org:4906268 2024-09-15T18:28:58+00:00 Property map collective variable as a usefultool for force field correction - analysis Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech 2021-06-07 https://doi.org/10.5281/zenodo.4906268 unknown Zenodo https://zenodo.org/communities/elixir-cz https://doi.org/10.5281/zenodo.4906267 https://doi.org/10.5281/zenodo.4906268 oai:zenodo.org:4906268 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode molecular dynamics simulation metadynamics molecular mechanics info:eu-repo/semantics/article 2021 ftzenodo https://doi.org/10.5281/zenodo.490626810.5281/zenodo.4906267 2024-07-27T01:56:22Z 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. Here we present input and output files for analysis by Plumed, R with Rmarkdown and Metadynminer. The analysis can be initialized by: plumed driver --plumed plumed.dat --ixtc trajectory.xtc R Markdown plot PDF can be gerated by: Rscript -e "rmarkdown::render('./Figures.Rmd')" Files: Figures.Rmd - Rmarkdown input file Figures.pdf - Rmarkdown output file aladip/vacuum/amber03/HILLS - Metadynamics hills file generated by Plumed aladip/vacuum/amber94/HILLS - Metadynamics hills file generated by Plumed aladip/vacuum/amber94to03/HILLS - Metadynamics hills file generated by Plumed aladip/water/correction/diffs_corrected.txt aladip/water/correction/diffs_uncorrected.txt imatinib/plumed.dat imatinib/COLVAR_corrected imatinib/COLVAR_uncorrected Article in Journal/Newspaper Orca Zenodo |
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molecular dynamics simulation metadynamics molecular mechanics |
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molecular dynamics simulation metadynamics molecular mechanics Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech Property map collective variable as a usefultool for force field correction - analysis |
topic_facet |
molecular dynamics simulation metadynamics molecular mechanics |
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. Here we present input and output files for analysis by Plumed, R with Rmarkdown and Metadynminer. The analysis can be initialized by: plumed driver --plumed plumed.dat --ixtc trajectory.xtc R Markdown plot PDF can be gerated by: Rscript -e "rmarkdown::render('./Figures.Rmd')" Files: Figures.Rmd - Rmarkdown input file Figures.pdf - Rmarkdown output file aladip/vacuum/amber03/HILLS - Metadynamics hills file generated by Plumed aladip/vacuum/amber94/HILLS - Metadynamics hills file generated by Plumed aladip/vacuum/amber94to03/HILLS - Metadynamics hills file generated by Plumed aladip/water/correction/diffs_corrected.txt aladip/water/correction/diffs_uncorrected.txt imatinib/plumed.dat imatinib/COLVAR_corrected imatinib/COLVAR_uncorrected |
format |
Article in Journal/Newspaper |
author |
Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech |
author_facet |
Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech |
author_sort |
Trapl, Dalibor |
title |
Property map collective variable as a usefultool for force field correction - analysis |
title_short |
Property map collective variable as a usefultool for force field correction - analysis |
title_full |
Property map collective variable as a usefultool for force field correction - analysis |
title_fullStr |
Property map collective variable as a usefultool for force field correction - analysis |
title_full_unstemmed |
Property map collective variable as a usefultool for force field correction - analysis |
title_sort |
property map collective variable as a usefultool for force field correction - analysis |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://doi.org/10.5281/zenodo.4906268 |
genre |
Orca |
genre_facet |
Orca |
op_relation |
https://zenodo.org/communities/elixir-cz https://doi.org/10.5281/zenodo.4906267 https://doi.org/10.5281/zenodo.4906268 oai:zenodo.org:4906268 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.490626810.5281/zenodo.4906267 |
_version_ |
1810470393185566720 |