YUP: A Molecular Simulation Program for Coarse-Grained and Multiscaled Models

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Abstract
Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently, and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multiscaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual nonlinear polymer, and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsids. We find that objects are easy to modify, extend, and redeploy. Thus, new classes of coarse-grained models can be implemented easily.