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feiglab / sars-cov-2-proteins

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M protein MD refinement #1

Open smsaladi opened 4 years ago

smsaladi commented 4 years ago

Would it be possible to share some snapshots of the MD carried out on protein M in the presence of a membrane?

feiglab commented 4 years ago

We are using MD for refinement but these are restrained simulations with a special force field. The only really meaningful output is the ensemble-averaged structure that we are providing. There is only limited value in our actual MD simulations and it would be misleading to make them available as they do not reflect unbiased Boltzmann sampling.

There are other groups that have made 'real' MD simulations of SARS-CoV-2 proteins available. See for example here: https://covid.molssi.org/

Alternatively, our refined models should be suitable as a starting point for unbiased simulations. Easy setup of such simulations is possible e.g. via CHARMM-GUI: http://charmm-gui.org