[ase-users] Calculating Transition Paths for Rare Events

[Daniel Sutton]

Dear ASE Users,

I would like to bring to your attention the following package that we have been developing here in the Mathematics Department at the University of Bath: https://github.com/suttond/GeometricMD <https://github.com/suttond/GeometricMD> (PyPi: geometricmd)

Given two configurations of a molecular system (such as a protein in two folded states, or a crystalline structure in two phases) our package, GeometricMD, computes the trajectory that joins them. The trajectory will solve Newton’s second law for the molecule where the potential and forces are determined by the get_potential_energy() method of the attached calculator object. It is designed to interface with ASE. Tutorials are provided on the website on how to use the code. At present it can perform NVT simulations. It can also perform NPT simulations where the atomistic system is periodic in all three space directions.

It performs this calculation using curve shortening techniques for the Maupertuis principle [1, 2, 3]. A feature of this method is that it lends itself naturally to parallelisation. Another feature is that since the Maupertuis principle is a geometric principle, it is possible to run simulations over significantly larger timescales than those accessible through step based methods. 

We have also released an alternative implementation here https://github.com/suttond/MODOI <https://github.com/suttond/MODOI> (PyPi: MODOI). This implementation uses TCP/IP to distribute the computing over a local network, rather than in multiple processes, making it possible perform computationally intensive simulations without a HPC cluster.

Thank you for reading,

Daniel Sutton

—
References:

[1] (http://arxiv.org/abs/1502.01741) A convergent string method: Existence and approximation for the Hamiltonian boundary-value problem. H. Schwetlick and J. Zimmer. Dynamical Systems, Number Theory and Applications: A Festschrift in Honor of Armin Leutbecher's 80th Birthday, to appear. 

[2] The computation of long time Hamiltonian trajectories for molecular systems via global geodesics. H. Schwetlick and J. Zimmer.  Numerical Mathematics and Advanced Applications 2011 (ENUMATH, Leicester), Springer, 227-234.

[3] (opus.bath.ac.uk/38797/1/UnivBath_PhD_2013_D_C_Sutton.pdf) Chapter 4, Microscopic Hamiltonian systems and their effective description. D.C. Sutton. Ph.D. Thesis, University of Bath.

 

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