Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics

  • Katarzyna Kulczycka-Mierzejewska
  • Joanna Trylska
  • Joanna SadlejEmail author
Original Paper


Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born–Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.


Antibiotics Lincosamides Clindamycin Born–Oppenheimer molecular dynamics BOMD Quantum mechanics/molecular mechanics QM/MM Full-atom molecular dynamics FAMD 



Computational resources were provided by the Interdisciplinary Centre for Mathematical and Computational Modelling of the University of Warsaw by grants G31-4 G31-13 and G59-9. The authors acknowledge support from the University of Warsaw (CeNT/BST), National Science Centre (DEC-2012/05/B/NZ1/00035 and UMO-2013/09/N/ST4/00932).

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Katarzyna Kulczycka-Mierzejewska
    • 1
    • 2
  • Joanna Trylska
    • 3
  • Joanna Sadlej
    • 4
    Email author
  1. 1.Interdisciplinary Centre for Mathematical and Computational ModellingUniversity of WarsawWarsawPoland
  2. 2.College of Inter-faculty Individual Studies in Mathematics and Natural ScienceUniversity of WarsawWarsawPoland
  3. 3.Centre of New TechnologiesUniversity of WarsawWarsawPoland
  4. 4.Faculty of ChemistryUniversity of WarsawWarsawPoland

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