Scientific results using RCCS

“Bucket brigade” of remdesivir in RNA-dependent RNA polymerase of SARS-CoV-2

　The process of remdesivir uptake into the protein (RNA-dependent RNA polymerase) that replicates the gene of SARS-CoV-2 was revealed by molecular dynamics simulations. Remdesivir has a phosphate group with a negative charge, and the binding site of RNA polymerase has Mg2+ ions. In addition, RNA polymerase has lysine residues, which are positively charged, in a line toward the binding site. It was found that the lysine residue attracts the phosphate group of remdesivir and passes it to the next lysine residue sequentially, transporting the drug to the binding site like a bucket brigade.

S. Tanimoto, S. G. Itoh, and H. Okumura: Biophys. J. (2021), DOI: 10.1016/j.bpj.2021.07.026, “Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2

Molecular simulations of functional dynamics in biomolecular machines

Functional dynamics plays an important role when biomolecular machines fulfill their functions. For example, transporter proteins transport their substrates across the membrane by changing their conformation between inward-open and outward-open conformations. Although it is difficult to directly simulate millisecond functional time of these biomolecular machines whose total atoms amount to several hundred thousand, we use techniques such as metadynamics or transition path sampling to uncover molecular mechanism of the functioning moments.

K. Okazaki, D. Wöhlert, J. Warnau, H. Jung, Ö. Yildiz, W. Kühlbrandt and G. Hummer, Nat. Commun. 10, 1742 (2019)

Divergent applications of ab initio reaction dynamics and automated reaction path search

Analyses of ab initio MD trajectories for gold cluster structural transformation based on the global reaction route map clarify the dynamic reaction route going beyond the IRC pathways, leading to a new concept of "reaction path-jumping."

T. Tsutsumi, Y. Harabuchi, Y. Ono, S. Maeda, and T. Taketsugu, Phys. Chem. Chem. Phys., 20, 1364 (2018).

Simulations of Catalytic Reactions on Surface

Amide compounds are widely used for fine chemicals, medical drugs, and agricultural chemicals. By using quantum chemical calculations on supercomputer, we clarified the origin of the catalytic activity of Nb2O5 surface which performs highly efficient amidation reactions.
P. Hirunsit, T. Toyao, S. M. A. H. Siddiki, K. Shimizu, M. Ehara, ChemPhysChem (2018).

Show list

Update Information

2021-08-19 Sep 22 (Wed) 0:30-1:30 AM: network access to RCCS temporarily unavailable

Due to the maintenance work, network access to RCCS will be unavailable for 30 minutes somewhere from 0:30 AM to 1:30 AM on Sep 22 (Wed). You can't login to the frontend nodes during the maintenance. Already submitted jobs won't be affected.
2021-08-18 Aug 26 (Thr) 9:00-17:00 NOUS scheduled maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Aug. 26 due to the sceduled maintenance. The service might be resumed earlier than the scheduled time, 17:00.
2021-07-13 July 13: temporary power failure of cooling system due to the lightning (Jul 20 update)

At around 18:50 on July 13th, temporary power failure of our cooling system (colling tower) occurred due to the lightning. Due to the trouble, this website went down and some of commands in RCCS system (such as showlim) had been unavailbale during July 13 20:00-21:00. Also, 6 of computation nodes went down. Those problems (excluding computation node ones) were fixed until July 13 22:00. File system, frontend nodes, and the other computation nodes were not seriously affected by the issue.
(Jul 20 update) CPU points of the following affected jobs were paid back.
2021-05-25 Error due to the new private key format of PuTTY 0.75 (PPK ver. 3)

WinSCP and other programs have trouble with new private key file create with PuTTY 0.75 default setting. This is due to a new private key format introduced in PuTTY 0.75. Please check workaround below if you see an error message like "PuTTY key format too new".
2021-05-14 FY2020 Usage Report (Deadline: Jun 1)

The deadline for FY2020 usage report is Tuesday, Jun 1. Details about the report can be found in this page. Please note that only the representative person can upload the report.
(May 20) We have fixed most of the errors of NOUS. Also, we have sent emails individually to representatives whose project is not yet correctly recognized in NOUS. In case you can't find "upload" button in your page of NOUS and don't receive email from RCCS even after May 20 13:30, please tell us via contact from or email. We are really sorry for the inconvenience.
2021-04-28 Thu May 13, 9:00-17:00 NOUS unavailable due to the maintenance

NOUS will be unavailable in Thursday, May 13, 9:00-17:00 due to the scheduled maintenance. You cannot submit new application/report during the period. (The restart time may vary.)
Subscribe to Front page feed