Re: [AMBER] How should I perform a long-time Simulated Annealing MD?

From: David A Case <>
Date: Wed, 4 Jul 2018 08:41:42 -0400

On Wed, Jul 04, 2018, wrote:
> And I have tried aMD and GaMD for several times and I can not get the
> right protein conformation. The protein has significant conformational
> change which has identified by X-ray. Does Amber has other enhenced
> sampling method can simulate the protein allosteric effect?

Expecting to see spontaneous allosteric conformational changes in a large
protein via MD simulations may be unrealistic. The time scale for many such
changes is on the microsecond to millisecond time scale (or longer), and are
hence not readily approached by brute force simulations. (And, of course,
current force fields may not properly describe all of these alternate
conformational basins.)

If you know a collective coordinate that would describe the change between
the two conformers, you could try any of several enhanced sampling
methods, from umbrella sampling to NFE (non-equilibrium free energy)
methods. The nudged elastic band method is sometimes helpful in finding
pathways between conformers. And you might learn something by starting a
simulation in the target state that was "identified by X-ray".

...hope this helps.....dac

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Received on Wed Jul 04 2018 - 06:00:05 PDT
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