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IBIsCO: A molecular dynamics simulation package for coarse‐grained simulation
Author(s) -
KarimiVarzaneh Hossein Ali,
Qian HuJun,
Chen Xiaoyu,
Carbone Paola,
MüllerPlathe Florian
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21717
Subject(s) - dissipative particle dynamics , thermostat , molecular dynamics , computer science , granularity , computational science , statistical physics , powerpc , parallel computing , dynamics (music) , degrees of freedom (physics and chemistry) , physics , computational chemistry , thermodynamics , chemistry , software , programming language , nuclear magnetic resonance , polymer , acoustics
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 (Müller‐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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011