1/1
2 files

Trajectory data for the toy-model simulation in "GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics"

figure
posted on 02.02.2021, 07:28 by Junichi Higo, Kota Kasahara, Ayumi Kusaka, Narutoshi Kamiya, Xie Qilin, Hayato Itaya, Takuya Takahashi, Ikuo Fukuda, Kentaro Morita, Yutaka Hata, Yoshifumi Fukunishi
traj.tar.gz:
The trajectory data for the test simulations of the virtual-system coupled Monte Carlo (VcMC) method, reported in the manuscript entitled "GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics". The simulation system consists of one particle in a cubic cell with the double-well potential field.

The data includes two sets of VcMC simulations: (i) a low temperature and (ii) a high temperature. The two directories in the top hierarchy, named "low_t" and "high_t", correspond to simulations in these two conditions, respectively. In these directories, there are directories named "1", "2", ... corresponding to the first, second ... iterations. In each of them, trajectories of 30 parallel runs of simulations were stored in the directories termed "n1", "n2", ..., "n30".

For each directory, two trajectory files, which are formatted as space-separated three column texts, are included. "lambda.out" records the real-space 3D coordinates with 1000-step interval. "ttpv_vcmd.out" records the virtual-system 3D coordinates (i.e., the indices to specify the zone to which the system belongs) with 10-step interval. Each row indicates the position of each frame.

Text files named "vcmd.inp" describes the definition of the virtual system.
1st line: the interval steps for virtual state transition trials.
2nd line: the dimension of the virtual state.
3rd line: the number of states in the first dimension.
the next 11 lines: the range of each zone in the first dimension of the virtual system.
the next 24 lines: information for the second and third dimensions of the virtual system.
the remaining lines: canonical probability, or weighting coefficient, for each virtual state. The first three values indicate the 3D coordinate in the virtual system. The fourth value is the canonical probability.

Figure (thumbnail.png):
The canonical probability in the 3D virtual system. This figure is reprinted from Figure 11 (a) in the original paper, licensed under CC BY-NC-SA 4.0.

Funding

The Development of Core Technologies for Innovative Drug Development Based Upon IT from Japan Agency for Medical Research and Development (AMED)

The Cooperative Research Program of the Institute for Protein Research, Osaka University, CR-19-05 and CR-20-05.

kinetic constants of molecular binding calculated from equilibrium

Japan Society for the Promotion of Science

Find out more...

Computational design of novel proteins with weak interactions

Japan Society for the Promotion of Science

Find out more...

Complex structure and affinity prediction among cancer vaccine peptides and immune related proteins

Japan Society for the Promotion of Science

Find out more...

History

Manuscript title

GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics

Article DOI

10.2142/biophysico.BSJ-2020008

Corresponding author email address

higo@protein.osaka-u.ac.jp