Re: nonuniform sampling in ABF

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jun 12 2018 - 17:09:56 CDT

Hi,

Haohao's answer is very good. I would also add that the long-time behavior
is uniform sampling, but for a biological system even those timescales are
very hard to achieve, so the convergence is local anyway. A way I like to
look at the sampling histograms is to calculate the associated effective
PMF, that is, 0.6*ln(N(x)), in kcal/mol at 300 K. Then I compare this
effective PMF to the calculated PMF from ABF. this tells me by how much the
free energy landscape has been flattened.

Best,
Jerome

On 12 June 2018 at 18:25, Haohao Fu <fhh2626_at_gmail.com> wrote:

> The problem is that the reaction coordinate model chosen is too simple to
> describe the process. Your definition of RC implies that the rotational
> movement and the conformational change of the proteins can be observed in
> the time scale of your simulation, which is not true.
>
> Just try to introduce some restraints to reduce the degrees of freedom
> (e.g. Orientation、polarPhi and polarTheta colvar) and discuss the effects
> of the restraints. See J. Chem. Theory Comput., 2017, 13 (11), 5173–5178
> and J. Chem. Theory Comput., 2013, 9 (1), 794–802 for some examples

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