期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 32, 期 7, 页码 1475-1487出版社
WILEY
DOI: 10.1002/jcc.21717
关键词
molecular dynamics simulation package; coarse-graining simulation; iterative Boltzmann inversion method
资金
- Alexander-von-Humboldt foundation
IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Muller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 1475-1487, 2011
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