TY - JOUR
T1 - Implementation of replica-exchange umbrella sampling in GAMESS
AU - Ito, Shingo
AU - Fedorov, Dmitri G.
AU - Okamoto, Yuko
AU - Irle, Stephan
N1 - Publisher Copyright:
© 2018
PY - 2018/7
Y1 - 2018/7
N2 - In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation.
AB - In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation.
KW - Density-functional tight-binding
KW - GAMESS-US
KW - Multidimensional replica-exchange method
KW - Replica-exchange molecular dynamics
KW - Replica-exchange umbrella sampling
KW - Umbrella sampling
UR - http://www.scopus.com/inward/record.url?scp=85044388557&partnerID=8YFLogxK
U2 - 10.1016/j.cpc.2018.01.014
DO - 10.1016/j.cpc.2018.01.014
M3 - Article
AN - SCOPUS:85044388557
SN - 0010-4655
VL - 228
SP - 152
EP - 162
JO - Computer Physics Communications
JF - Computer Physics Communications
ER -