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Highly parallel QM/MM interface

Many quantum biological applications (e.g. simulations of enzymatic reactions) usually require dealing with large systems (typically of the order of 104 – 105 atoms), making first principles quantum mechanical strategies far too costly. This motivates using a multiscale approach, in which the part of the system that is of particular interest (e.g. the active site of an enzymatic reaction) is treated at quantum level (QM part), while the rest of the system is handled by a classical force field (MM part). Such a hybrid QM/MM approach allows a significant decrease of the size of the computationally expensive part, while keeping the ability to represent the processes that can only be treated by quantum chemistry (e.g. chemical reactions). Unfortunately, most of the current implementations of QM/MM codes do not scale very well, limiting tremendously the domain of applications of this otherwise very powerful approach. In an effort at coding a truly HPC QM/MM code, we are focusing on building a QM/MM coupling scheme based on the CPMD code. This is a highly efficient massively parallel first-principles (quantum) molecular dynamics software package. It can scale up to a few million threads with extremely high efficiency (see e.g. here). The old built-in QM/MM implementation of CPMD has a set of issues that prevent its usage on large-scale neurobiological applications. First, the scalability of the MM description is limited, thus, simulating large systems becomes time consuming. Second, the number of classical force fields that can be used is restricted to AMBER and GROMOS96 formats. Finally, because of the tight coupling of CPMD to routines from the GROMOS96 code, which is used to handle the classical part of the simulation, the user needs to buy a commercial GROMOS96 license in order to be able to run QM/MM simulations.

We have recently developed a new QM/MM platform (MiMiC) [1,2], which uses a loose coupling scheme to connect CPMD with in principle any client MM code, and in particular we have explicitly coupled it to the GROMACS code [1]. The loose coupling requires the use of a communication layer in order to establish data interaction between the independent codes. This approach allows us to benefit from the highly efficient parallelization schemes of both CPMD and GROMACS codes [2]. It also provides us with a flexible and easily extendable framework that potentially will allow the support of any kind of MM code and any type of force field. Finally, the loose coupling allows overriding licensing issues that can arise when coupled codes have not permissive licenses.

This MiMiC project is performed in collaboration with the group of Prof. U. Rothlisberger (EPFL Lausanne, Switzerland), Dr. J. M. Haugaard Olsen (University of Southern Denmark, Odense M, Denmark and Dr. S. Meloni (Sapienza University Rome, Italy), and it is supported by the European BioExcel Center of Excellence and the European Joint Doctorate HPC-LEAP.


References

  1. Olsen J M H, Bolnykh V, Meloni S, Ippoliti E, Bircher M P, Carloni P, Rothlisberger U. (2019) MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry. J. Chem. Theory Comput. 15(6): 3810-3823. doi: 10.1021/acs.jctc.9b00093
  2. Bolnykh V, Olsen J M H, Meloni S, Bircher M P, Ippoliti E, Carloni P, Rothlisberger U. (2019) Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC. J. Chem. Theory Comput. 15(10): 5601-5613. doi: 10.1021/acs.jctc.9b00424

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