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Manuscript Title: A Generic Implementation of Replica Exchange with Solute Tempering (REST2) Algorithm in NAMD for Complex Biophysical Simulations
Authors: Sunhwan Jo, Wei Jiang
Program title: REST2-NAMD
Catalogue identifier: AEXX_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 197(2015)304
Programming language: C/C++, Tcl8.5.
Computer: Not computer specific.
Operating system: Any.
Has the code been vectorised or parallelized?: Yes, MPI and/or PAMI parallelized depending on machine system software; ≥ 8192 cores used on IBM Blue Gene/Q
Keywords: REST2, NAMD, Tcl, Free Energy Calculation.
Classification: 3.

External routines: NAMD 2.10 (http://www.ks.uiuc.edu/Research/namd/)

Nature of problem:
A generic implementation providing user-friendly API including input file preparation and performing replica exchange, and high frequency exchange attempt frequency with minimal communication overhead.

Solution method:
The rescaling procedure of force field parameters controlling REST2 is implemented into NAMD at the source code level. A user can conveniently select hot region through VMD and write the selection information into a PDB file. The rescaling keyword/parameter is written in NAMD Tcl script interface that enables an on-the-fly simulation parameter change. The implementation of REST2 is within communication-enabled Tcl script built on top of Charm++, thus communication overhead of an exchange attempt is vanishingly small.

Running time:
30 min - 60 min