On Fri, Jun 27, 2014 at 5:27 AM, Suman Chakrabarty
chakrabarty.su...@gmail.com wrote:
Hello!
1. It seems I have encountered a minor bug (?) in repl_ex.c for
version 4.6.x (for NPT simulations only):
Line 880 (in version 4.6.5):
fprintf(fplog, dpV = %10.3e d = %10.3e\nb, dpV, delta +
dpV);
should be:
fprintf(fplog, dpV = %10.3e d = %10.3e\n, dpV, delta +
dpV);
The extra b results into lines like this in the log file:
bRepl ex 0123456789 10 11
12 x 13 14 x 15 16 x 17 18 19 20 x 21
While the REMD itself runs fine, the lines containing bRepl ex are
never parsed by the demux.pl script. So, only half of the exchanges
are analyzed by the script.
Yes. This will be fixed in 5.0. You can safely hack out the excess b in
the source if you want a fix in 4.6.x
2. The related question: In the log file, the dPV corrections are
reported only every alternate exchange attempts: (I have kept only a
relevant trimmed part below)
Replica exchange at step 2000 time 4
Repl ex 012345 x 67 x 89 x 10
Replica exchange at step 3000 time 6
Repl 0 - 1 dE_term = 6.670e-01 (kT)
dpV = -3.918e-05 d = 6.669e-01
bRepl ex 0 x 12345678 x 9 10
Why is this necessary? I hope it doesn't mean the correction is being
applied every alternate attempt (I have not checked this part of the
code yet).
Such output is only done from the lower-numbered replica, and the sets of
replicas that exchange alternate between subsequent exchange attempts. You
can only see the full situation by considering all the .log files.
Is it safe to use NPT REMD with the current version of the code? If I
just apply the above correction, and use demux.pl to analyze ALL
exchange attempts, is it still valid? Please confirm.
I expect so. Note that all simulation users should be doing their own
sanity checks, such as confirming that your settings produce statistically
indistinguishable results on (say) some water boxes with and without
-replex on. Nobody else has tested your exact system ;-) Or
http://dx.doi.org/10.1021/ct300688p
Mark
Thanks,
Suman.
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