Parallel tempering Monte Carlo in LAMMPS.

Rintoul, Mark Daniel ; Plimpton, Steven James ; Sears, Mark P.

Sandia National Laboratories

关键词: 99 General And Miscellaneous//Mathematics, Computing, And Information Science;    Computerized Simulation;    L Codes;    Parallel Processing;    Monte Carlo Method;   

DOI  :  10.2172/918289
RP-ID  :  SAND2003-4113
RP-ID  :  AC04-94AL85000
RP-ID  :  918289

美国|英语

来源: UNT Digital Library

【 摘 要 】

We present here the details of the implementation of the parallel tempering Monte Carlo technique into a LAMMPS, a heavily used massively parallel molecular dynamics code at Sandia. This technique allows for many replicas of a system to be run at different simulation temperatures. At various points in the simulation, configurations can be swapped between different temperature environments and then continued. This allows for large regions of energy space to be sampled very quickly, and allows for minimum energy configurations to emerge in very complex systems, such as large biomolecular systems. By including this algorithm into an existing code, we immediately gain all of the previous work that had been put into LAMMPS, and allow this technique to quickly be available to the entire Sandia and international LAMMPS community. Finally, we present an example of this code applied to folding a small protein.