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...
| Main Authors: | , , , , , , |
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| Format: | Article in Journal/Newspaper |
| Language: | unknown |
| Published: |
2021
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| Subjects: | |
| Online Access: | https://zenodo.org/record/4906268 https://doi.org/10.5281/zenodo.4906268 |
| Summary: | 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 |
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