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Scientific results using RCCS

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).

Asymmetry of amyloid fibrils: Molecular Dynamics Simulations

Alzheimer’s disease, one of dementia, is caused by amyloid fibrils of amyloid-β (Aβ) peptides. It has been known that the Aβ amyloid fibrils extend only in one direction, but the reason has not been clarified. We found that the structure and fluctuation of the Aβ amyloid fibrils differ between the right and left ends by molecular dynamics simulations and clarified that this is the reason for the unidirectionality of the amyloid-fibril elongation. This result will be applied to develop inhibitors for the causative substance of the Alzheimer's disease.

H. Okumura and S. G. Itoh, Sci. Rep. 6 (2016) 38422 (9 pages).

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Update Information

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.)
2020-08-19 New inquiry address: rccs-admin(at)ims.ac.jp (former address ccadm(at)draco.ims.ac.jp is also still available)

We have prepared a new inquiry address rccs-admin(at)ims.ac.jp (replace (at) with @). Source address of RCCS mail news and answers to your questions will be gradually switching to this new address. Former inqury address ccadm(at)draco.ims.ac.jp (replace (at) with @) is still also available. Thank you for your cooperation.
2020-08-03 NOUS Scheduled System Maintenance

The NOUS system will be shut down during the following period. Please note that no new applications will be accepted during this period.
    August 13, 2020 09:00-17:00
The service will be suspended for approximately 8 hours, and will be resumed as soon as the work is completed.
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