About the scope of show_replicas.vmd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Sep 19 2013 - 01:48:16 CDT

I posed the same question to the vmd forum but probably is to the namd
forum pertinent for the question.

Thus, I carried out a short T-remd on alanin with 8 replicas, as provided
by namd_2.9. I used the final namd-provided folded pdb for comparison. The
script show_replicas.vmd with these replicas warned "not converged".

With my peptide, 32 replicas, after 370,000 steps still far from
convergence, I used, for the vmd comparison, the starting unfolded.pdb also
as a fake folded.pdb. In this case, show_replicas.vmd did not raise any
warning. Looking also at the code, it seems to me that show_replicas.vmd
assumes, as a criterion of convergence, the comparison of the various
replicas with the pdb file that you give as folded peptide in the
fold.peptide.conf file. That works if your T-remd is just devised to check
if you are able to reproduce an experimentally defined situation.

Suppose instead that your T-remd is devised to search for the best
conformation, or cluster of conformations, for an experimentally undefined
peptide. I can imagine many situations where the experimental approach is
problematic. Then you need a real criterion of convergence of yor T-remd,
before starting to examine the (sorted) same-T replicas. Obviously, a
reliable criterion of convergence is that what you get must be the same
from each replica, for example that the average structure is the same from
all replicas.

Therefore, I got the impression that the warning "not converged" raised by
show_replicas.vmd is misleading. Is any script available to check when any
replica gives the same answer.

Thanks for advice, even if showing that I am wrong.

francesco pietra

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