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the scaling, 8 replicas are amply sufficient for obtaining a good exchange rate (see T able 1). .
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  • It is based on softening nonbonded ligand-receptor interactions along the replicas and one reference replica under the control of the original force field.
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  • The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques.
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    The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques.

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    Here we apply the binding energy distribution analysis method (BEDAM) to obtain the binding free energy and binding energy distributions of this complex.