MiMiCPy-FM: a user-friendly force matching tool for extending the time scale of QM/MM MD MiMiC simulations

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Atomistic molecular dynamics (MD) simulations were performed on isocitrate dehydrogenase 1 (IDH1), a dimeric, magnesium-dependent enzyme that catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate (αKG). The force field parameters used to simulate the chain B monomer were derived from QM/MM calculations combined with force matching.

Authors 9

1. Sachin Shivakumar
2. Giorgia Frumenzio
3. Francesco Musiani

   University of Bologna

   Affiliation as printed

   University of Bologna

4. Fabio Affinito

   Cineca

   Affiliation as printed

   Cineca

5. Emiliano Ippoliti

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

6. Barath Raghavan
7. Giulia Rossetti
8. Davide Mandelli

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

9. Paolo Carloni Aachen

   RWTH Aachen University

   Affiliation as printed

   Rheinisch Westfälische Technische Hochschule Aachen RWTH Aachen Fakultät für Mathematik Informatik und Naturwissenschaften