Graham, James, Andrew, Essex, Jonathan and Khalid, Syma (2017) PyCGTOOL: automated generation of coarse-grained molecular dynamics models from atomistic trajectories. Journal of Chemical Information and Modeling, 57 (4), 650-656. (doi:10.1021/acs.jcim.7b00096).
Abstract
Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of internal coordinates directly from atomistic molecular dynamics simulation trajectories. The derivation of bespoke parameters from atomistic simulations improves the quality of the CG model compared to the use of generic parameters derived from other molecules, while automation greatly reduces the time required. The ease of configuration of PyCGTOOL enables the rapid investigation of multiple atom-to-bead mappings and topologies. Although we present PyCGTOOL used in combination with the GROMACS molecular dynamics engine its use of standard trajectory input libraries means that it is in principle compatible with other software. The software is available from the URL https://github.com/jag1g13/pycgtool as the following doi: 10.5281/zenodo.259330.
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- Faculties (pre 2018 reorg) > Faculty of Natural and Environmental Sciences (pre 2018 reorg) > Chemistry (pre 2018 reorg)
Current Faculties > Faculty of Engineering and Physical Sciences > School of Chemistry > Chemistry (pre 2018 reorg)
School of Chemistry > Chemistry (pre 2018 reorg) - Faculties (pre 2018 reorg) > Faculty of Physical Sciences and Engineering (pre 2018 reorg) > Electronics & Computer Science (pre 2018 reorg)
Current Faculties > Faculty of Engineering and Physical Sciences > School of Electronics and Computer Science > Electronics & Computer Science (pre 2018 reorg)
School of Electronics and Computer Science > Electronics & Computer Science (pre 2018 reorg) - Faculties (pre 2018 reorg) > Faculty of Natural and Environmental Sciences (pre 2018 reorg) > Chemistry (pre 2018 reorg) > Computational Systems Chemistry (pre 2018 reorg)
Current Faculties > Faculty of Engineering and Physical Sciences > School of Chemistry > Chemistry (pre 2018 reorg) > Computational Systems Chemistry (pre 2018 reorg)
School of Chemistry > Chemistry (pre 2018 reorg) > Computational Systems Chemistry (pre 2018 reorg)
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