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Property map collective variable as a useful tool for force field correction

Dalibor Trapl1*, Martin Krupička2*, Vladimir Višňovský3*, Jana Hozzová3*, Jaroslav Oľha3*, Aleš Křenek3*, Vojtěch Spiwok4*

1 Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic

2 Department of Organic Chemistry, University of Chemistry and Technology, Prague, Czech Republic

3 Institute of Computer Science, Masaryk University, Brno, Czech Republic

4 Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague

* Corresponding authors emails: traplda@vscht.cz, Martin.Krupicka@vscht.cz, 467814@muni.cz, hozzova@ics.muni.cz, olha@ics.muni.cz, ljocha@ics.muni.cz, spiwokv@vscht.cz
DOI10.24435/materialscloud:yp-51 [version v1]

Publication date: Jun 01, 2021

How to cite this record

Dalibor Trapl, Martin Krupička, Vladimir Višňovský, Jana Hozzová, Jaroslav Oľha, Aleš Křenek, Vojtěch Spiwok, Property map collective variable as a useful tool for force field correction, Materials Cloud Archive 2021.84 (2021), doi: 10.24435/materialscloud:yp-51.

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.

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Files

File name Size Description
propertymapff.zip
MD5md5:f88e68d79d3d677188fc277356bcae94
108.1 MiB Input files and scripts to reproduce simulations
README
MD5md5:8b512f7f16f70b5785698401d7e88a9a
7.3 KiB README file
md5sum.txt
MD5md5:8fc7bffe7dceee6317cbf3f95f0fcc8f
31.6 KiB File fingeprtints by md5sum

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Journal reference (Paper in which the method is described)
D. Trapl, M. Krupička, V. Višňovský, J. Hozzová, J. Oľha, Aa Křenek, V. Spiwok, submitted (2021).

Keywords

molecular dynamics simulation molecular mechanics DFT free energy

Version history:

2021.157 (version v2) Oct 05, 2021 DOI10.24435/materialscloud:bx-gb
2021.84 (version v1) [This version] Jun 01, 2021 DOI10.24435/materialscloud:yp-51