metadynamics in openmm 7.4

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Omar Abuyaman
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Joined: Mon Apr 22, 2019 11:12 am

metadynamics in openmm 7.4

Post by Omar Abuyaman » Sun Sep 15, 2019 1:00 am

Hi
I would like to estimate the binding affinity of protein-ligand interaction. Can you please tell me how to run metadynamics of the complex. after i do the metadynamics , is there any function to calculate the free energy or i should do manual calculations.
Thanks
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Peter Eastman
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Re: metadynamics in openmm 7.4

Post by Peter Eastman » Sun Sep 15, 2019 12:23 pm

If you want to do free energy calculations, you might want to look at Yank (http://getyank.org/latest/). It's specifically designed for doing that.
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Omar Abuyaman
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Re: metadynamics in openmm 7.4

Post by Omar Abuyaman » Mon Sep 16, 2019 1:46 am

Thanks :)
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