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Center for High Performance Computing
Research Computing and Data Support for the University
In addition to deploying and operating high-performance computational resources and providing advanced user support and training, CHPC serves as an expert team to broadly support the increasingly diverse research computing and data needs on campus. These needs include support for big data, big data movement, data analytics, security, virtual machines, Windows science application servers, protected environments for data mining and analysis of protected health information, advanced networking, and more.
If you are new to the CHPC, the best place to learn about CHPC resources and policies is our Getting Started page.
Have a question? Please check our Frequently Asked Questions page and contact us if you require assistance or have further questions or concerns.
Upcoming Events:
Update to redwood idle session management following August 20, 2024 downtime
Posted September 3rd, 2024
Redwood Cluster Operating System Updated to Rocky Linux 8.10
Posted August 21st, 2024
Allocation Requests for Fall 2024 are Due September 1st, 2024
Posted August 7th, 2024
Allocation Requests for Summer 2024 are Due June 1st, 2024
Posted May 1st, 2024
CHPC Downtime: Tuesday March 5 starting at 7:30am
Posted February 8th, 2024
Two upcoming security related changes
Posted February 6th, 2024
Allocation Requests for Spring 2024 are Due March 1st, 2024
Posted February 1st, 2024
CHPC ANNOUNCEMENT: Change in top level home directory permission settings
Posted December 14th, 2023
CHPC Spring 2024 Presentation Schedule Now Available
CHPC PE DOWNTIME: Partial Protected Environment Downtime -- Oct 24-25, 2023
Posted October 18th, 2023
CHPC INFORMATION: MATLAB and Ansys updates
Posted September 22, 2023
CHPC SECURITY REMINDER
Posted September 8th, 2023
CHPC is reaching out to remind our users of their responsibility to understand what the software being used is doing, especially software that you download, install, or compile yourself. Read More...News History...
Structures and Dynamics of DNA Mini-Dumbbells are Force Field Dependent
By Lauren Winkler, Rodrigo Galindo-Murillo, Thomas E. Cheatham III.
Department of Medicinal Chemistry, College of Pharmacy, University of Utah
Resources from the Center for High Performance Computing were used to evaluate the influence of chosen force fields on Molecular Dynamics (MD) simulations of non-duplex DNA structures.
Flexible nucleic acid structures can be challenging to accurately resolve with currently available experimental structural determination techniques. MD simulations can be implemented to complement experimental techniques and have shown great success in modeling duplex DNA structures. Currently, noncanonical (non-duplex) structures have proven quite challenging to accurately replicate with respect to experimental structures. These structures are more sensitive to the balances of inter- and intra- molecular forces including charge interactions, hydrogen bonding, stacking contacts, and backbone flexibility, to name a few. In simulations, the forces are represented as “force fields” and small differences between force fields can lead to large differences in the simulations. In this work, currently available nucleic acid force fields are evaluated using a flexible, yet stable model system: the DNA mini-dumbbell. Prior to MD simulations, NMR re-refinement was accomplished using improved refinement techniques in explicit solvent to yield DNA mini-dumbbell structures that better agree with each other among the newly determined PDB snapshots, with the NMR data itself, as well as the unrestrained simulation data. Starting from newly determined structures, a total aggregate of over 800 µs of production data between 2 DNA mini-dumbbell sequences and 8 force fields was collected to compare to these newly refined structures. The force fields tested spanned from traditional Amber force fields: bsc0, bsc1, OL15, and OL21; to Charmm force fields: Charmm36 and the Drude polarizable force field; as well as force fields from independent developers: Tumuc1 and CuFix/NBFix. The results indicated slight variations not only between the different force fields, but also between the sequences. Surprisingly, many of the recently developed force fields generated structures in good agreement with experiments. Yet, each of the force fields provided a different distribution of potentially anomalous structures.
To find out more about this project, read the paper in the Journal of Computation and Theoretical Chemistry.
System Status
General Environment
General Nodes | ||
---|---|---|
system | cores | % util. |
kingspeak | 964/972 | 99.18% |
notchpeak | 2926/3212 | 91.1% |
lonepeak | 769/3012 | 25.53% |
Owner/Restricted Nodes | ||
system | cores | % util. |
ash | 1152/1152 | 100% |
notchpeak | 16543/21940 | 75.4% |
kingspeak | 3932/5340 | 73.63% |
lonepeak | 416/416 | 100% |
Protected Environment
General Nodes | ||
---|---|---|
system | cores | % util. |
redwood | 556/628 | 88.54% |
Owner/Restricted Nodes | ||
system | cores | % util. |
redwood | 4825/6472 | 74.55% |