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- How to calculate the binding energy in the Martini coarse-grained MD simulation?
How to calculate the binding energy in the Martini coarse-grained MD simulation?
- Tim
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3 years 10 months ago - 3 years 10 months 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
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: 3 years 10 months ago by Tim.
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- riccardo
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3 years 10 months ago #8608
by riccardo
Replied by riccardo on topic How to calculate the binding energy in the Martini coarse-grained MD simulation?
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
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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- How to calculate the binding energy in the Martini coarse-grained MD simulation?
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