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slashdave t1_jbvxc0t wrote

Reply to comment by danby in What exactly is going on when a protein (or other molecule) binds with a receptor? by Eat-A-Torus

Molecular dynamics is adequate in most simple cases. You could say we are limited with what kind of computing power we can apply in complex systems.

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danby t1_jbz2kzo wrote

Why on earth would we be only interested in simple cases?

MD is fine in many cases (very, very good in some) but it is absolutely not sufficient to fully model and understand the dynamics of proteins. We know the forcefields we have are lossy and not great for many applications when it comes to proteins. Simulations of long time spans or large protein rearrangements are generally very poor.

> You could say we are limited with what kind of computing power we can apply in complex systems.

Well yeah we limited there.

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slashdave t1_jbz9uck wrote

>Why on earth would we be only interested in simple cases?

We aren't. The statement "we don't have a good way of modeling the dynamics of proteins" isn't correct. If you want to amend that to "complex systems", you might have an argument, but there are also accelerated MD methods that are quite effective.

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