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Welcome
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We should all understand and follow the ARCHER2 Code of Conduct to ensure this course is conducted in the best teaching environment.
The course will be flexible to best meet the learning needs of the attendees.
Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees.
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Connecting to ARCHER2 and transferring data
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ARCHER2’s login address is login.archer2.ac.uk.
The password policy for ARCHER2 is well documented.
There are a number of ways to transfer data to/from ARCHER2.
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Preparing a GROMACS system
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Creating Gromacs topology files
Creating your simulation box
Solvating a system
Adding ions to neurtalise your system
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Running GROMACS simulations on ARCHER2
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GROMACS simulation parameters are defined in a .mdp file
GROMACS simulations are prepared using the grompp tool.
GROMACS simulations are run using the mdrun command.
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Visualising and analysing simulation data
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Use of gmx energy, make_ndx, rms
System visualisation in vmd
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Performance: getting the best bang for your (computational) buck
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Hybrid MPI with OpenMP does affect performance.
When running hybrid jobs, placement across NUMA regions is important.
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Next steps
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The GROMACS manual provides a number of useful resources for learning about GROMACS.
You will retain access to ARCHER2 for a while – please make use of it to test GROMACS more.
You can get access to ARCHER2 resources via a number of different routes.
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