Project Application Details

ARCHIE Project title: 12GB
Project PI: 295 Cathedral Street
Department: 01/10/2012
Address: 295 Cathedral Street, , open-source software, G1 1XL
Relevant industrial collaborations:
Existing relevant KTP activities:
Does the PI require to run calculations? 9
Number of users involved in the project: Depending on allocated nodes – can run 1 job per 12 processors, 8000 jobs.
User 1 details:

Mr. Pim Frederix
PhD student – University of Strathclyde
Pure & Applied Chemistry / Biomolecular and Chemical Physics
Phone +44 (0) 141 552 3059
Email pim.frederix@strath.ac.uk

Service level requested:
ARCHIE Project description: 12GB
Potential output of the project:

The most obvious result of the study will be interesting potential candidates for new biomaterials, with uses in e.g. the cell culture field. Our lab has identified a few interesting examples of tripeptides, but it’s impossible to test all combinations. Together with our revised screening protocol, this should provide an interesting result and method for the biomaterials community which we will publish.
In the long run, we are not only trying to find potential peptide materials, but also use this methodology to slowly bridge the gap towards the discovery of short self-replicating peptides and oligopeptide enzymes, which have played a role in the origin of life. For example, our lab has recently identified some 12-mer peptides by an experimental screening protocol that possess amide bond breakage/condensation catalytic activity.

Project start date: 01/10/2012
Duration of the project: Depending on allocated nodes – can run 1 job per 12 processors, 8000 jobs.
Total CPU time required (in hours): 160000
CPU hours required by typical job: 9
Approximate amount of data created per job (in GB):
Approximate amount of data created per project: 12GB
Funding Agency Grant Reference No:
pFact ID:
RKES ID:
Software required for the project: open-source software
Software required to be installed for the project: Gromacs
Experience in using software package 1:
Software required to be installed for the project: VMD
Experience in using software package 2: 9
Software required to be installed for the project:
Experience in using software package 3: 1
Training required:
Other training required:
Experience in using HPC: 6