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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Bibliographic Details
Main Authors: Trapl, Dalibor, Krupička, Martin, Višňovský, Vladimir, Hozzová, Jana, Oľha, Jaroslav, Křenek, Aleš, Spiwok, Vojtěch
Format: Dataset
Language:English
Published: Materials Cloud 2021
Subjects:
molecular dynamics simulation
molecular mechanics
DFT
free energy
Lambda
Orca
Online Access:https://dx.doi.org/10.24435/materialscloud:bx-gb
https://archive.materialscloud.org/record/2021.157
Description
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. DFTB/MM simulation was carried out in CP2K 7.1. 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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