When an important process of a molecular system occurs via a combination of two or more rare events, which occur almost independently to one another, computational sampling for the important process is difficult. Here, to sample such a process effectively, we developed a new method, named the “multi-dimensional Virtual-system coupled Monte Carlo (multi-dimensional-VcMC)” method, where the system interacts with a virtual system expressed by two or more virtual coordinates. Each virtual coordinate controls sampling along a reaction coordinate. By setting multiple reaction coordinates to be related to the corresponding rare events, sampling of the important process can be enhanced. An advantage of multi-dimensional-VcMC is its simplicity: Namely, the conformation moves widely in the multi-dimensional reaction coordinate space without knowledge of canonical distribution functions of the system. To examine the effectiveness of the algorithm, we introduced a toy model where two molecules (receptor and its ligand) bind and unbind to each other. The receptor has a deep binding pocket, to which the ligand enters for binding. Furthermore, a gate is set at the entrance of the pocket, and the gate is usually closed. Thus, the molecular binding takes place via the two events: ligand approach to the pocket and gate opening. In two-dimensional (2D)-VcMC, the two molecules exhibited repeated binding and unbinding, and an equilibrated distribution was obtained as expected. A conventional canonical simulation, which was 200 times longer than 2D-VcMC, failed in sampling the binding/unbinding effectively. The current method is applicable to various biological systems.
Skip Nav Destination
Article navigation
7 October 2017
Research Article|
October 03 2017
Multi-dimensional virtual system introduced to enhance canonical sampling
Junichi Higo;
Junichi Higo
a)
1
Institute for Protein Research, Osaka University
, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
Search for other works by this author on:
Kota Kasahara
;
Kota Kasahara
2
College of Life Sciences, Ritsumeikan University
, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
Search for other works by this author on:
Haruki Nakamura
Haruki Nakamura
1
Institute for Protein Research, Osaka University
, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
Search for other works by this author on:
a)
Electronic mail: higo@protein.osaka-u.ac.jp
J. Chem. Phys. 147, 134102 (2017)
Article history
Received:
June 02 2017
Accepted:
September 13 2017
Citation
Junichi Higo, Kota Kasahara, Haruki Nakamura; Multi-dimensional virtual system introduced to enhance canonical sampling. J. Chem. Phys. 7 October 2017; 147 (13): 134102. https://doi.org/10.1063/1.4986129
Download citation file:
Sign in
Don't already have an account? Register
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Sign in via your Institution
Sign in via your InstitutionPay-Per-View Access
$40.00