REIN is an interface program for multi-dimensional replica-exchange molecular dynamics (MREMD) simulations. This program uses parallelized MD packages (currently, only MARBLE and NAMD are available) as MD engines without any modifications in MREMD simulations. This package includes the REIN main program as well as three software (input_builder, batch_builder, and remd_converter). REIN was written in Fortran95/2003 with MPI library and is distributed as free software under GPL version 3 license.



Naoyuki Miyashita (RIKEN Quantitative Biology Center (QBiC))
Yuji Sugita (RIKEN Theoretical Molecular Science (TMS))


Dr. Suyong Re (RIKEN TMS)
Mr. Norio Takase (Isogo Soft)

Principal Paper

[1] Naoyuki Miyashita, Suyong Re, Yuji Sugita, “REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function”, International Journal of Quantum Chemistry, (2014) accepted


REIN (ISLiM web page)


GPL v.3


twitter @rein_devel (
e-mail yukimya+rein{at}gmail.comĀ (change {at} to @)


02/26/2014 version 1.0.4
10/10/2012 version 1.0.0

Brief usage

See also file for detail.

Brief usage page


Research and Development of Next-Generation Intergrated Simulation of Living Matter (ISLiM), a part of the Development and Use of the Next-Generation Supercomputer Project of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan
RIKEN Quantitative Biology Center (QBiC)