From: Yasser Bruno Ruiz Blanco (ybruizblanco_at_gmail.com)
Date: Wed Jun 13 2018 - 06:04:10 CDT
I am running cpH MD and curiosly looking at report of the number of
attempts per residue after finishing some short runs (~200 cycles with 157
titratable residues = max number of attempts, 10 000 switching steps and
5000 standard simulation steps)
I understand this report refers to actual switching attempt computing the
alchemical transformations, and not just to the prior selection attempts
that can be neglected by the intrinsic Ka algorithms
Given I did not set any particular intrinsic Ka value for any of the
residues in the protein, I would expect NO effect of the intrinsic Ka
filter among residues of the same type. (i.e. I expect that all ASP are
sampled evenly or at least tend to so...)
Interestingly I am seen that the sampling after 200 cycles is almost
concentrated in a few (2 or 3) of the 157 residues.
Is this a behavior that has been observed before? Note, the sampling is not
fixed among the same 2 or 3 residues, but it is a fact that within 200
cycles the sampling that I got is extremely unhomogenuos within the same
residue type. Which is something that I would not expect if the residues
are selected randomly...
I'll thanks your comments.
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