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Trajectory data generated by a virtual-system coupled canonical molecular dynamics simulation with a coarse-grained model of glutamine-octapeptide dimer.

dataset
posted on 11.12.2020, 00:44 by Kota KasaharaKota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki NakamuraHaruki Nakamura, Takuya Takahashi, Junichi Higo

The trajectory data of the coarse-grained molecular dynamics simulation with the glutamine-octapeptide dimer generated by myPresto/omegagene.

The details of simulation is reported in the manuscript "myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling" (doi: 10.2142/biophysico.BSJ-2020013)

The file "md.trr" is recorded in GROMACS .trr format, which can be visualized by using some standard molecular viewers such as VMD (https://www.ks.uiuc.edu/Research/vmd/)

We recommend visualize the trajectory by using "VDW" or "points" representations for "Drawing Method". The methods depending on connectivity information, e.g., "NewCartoon" and "lines", are not working because of coarse graining.

This file included the 10,000 snapshots analyzed in the "Example" section of the manuscript.

As described in the manuscript, 10 independent runs of 10^7 steps of simulation were done as production runs. The snapshots were recorded at every 10,000 steps, and 1,000 snapshots were recorded for each run. The "md.trr" file was generated by concatenating these snapshots over 10 runs.

The file "q8dimer.pdb" is the initial coordinates of the simulation model. Each atom represents a bead corresponding to one amino acid residue.

The cell-dimension of cubic periodic boundary cell is 60 Å.


Funding

Computational design of novel proteins with weak interactions

Japan Society for the Promotion of Science

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kinetic constants of molecular binding calculated from equilibrium

Japan Society for the Promotion of Science

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Study of the phosphorylation latch mechanism for the transcriptional regulation via intrinsically disordered regions

Japan Society for the Promotion of Science

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History

Manuscript title

myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling

Article DOI

10.2142/biophysico.BSJ-2020013

Corresponding author email address

ktkshr@fc.ritsumei.ac.jp