normal How to calculate the binding energy in the Martini coarse-grained MD simulation?

  • Tim
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1 month 2 weeks ago - 1 month 2 weeks ago #8605 by Tim
Hi everyone,

I want to calculate the binding energy between the protein and the solid surface in Martini coarse-grained MD simulations conducted by Gromacs.

Could you tell me how to do that?

Many thanks, and best wishes.

Tim
Last edit: 1 month 2 weeks ago by Tim.

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1 month 2 weeks ago #8608 by riccardo
Hi Tim,

One way to do this could be by using umbrella sampling (US) - see here for our tutorial (on a much simpler system): cgmartini.nl/index.php/tutorials-general...ues#UmbrellaSampling
or metadynamics (again also shown in one of our tutorials: cgmartini.nl/index.php/tutorials-general...on-gmx5/metadynamics ).

Depending on how big is your protein, this may require quite some sampling. Here's a recent example using US - most probably more challenging than your case - have a look: www.nature.com/articles/s41467-020-15554-9

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