Hello experts,
I have done replica exchange simulations for two alanine-based polypeptides,
using ff99SB force field under NPT condition.
The number of replicas are 40 and 46 for each case.
(273 K to 490 K, 273 K to 536 K)
The initial conformation is helical and the trajectory is 20 ns long for every replica.
The taup and tautp values are 1 ps and 0.1 ps,
and the exange between replicas is done every 1 ps.
I have some questions on the convergence criteria in replica exchange simulations,
due to the following results.
The helical contents are severely fluctuating as expected,
but constantly decreasing and almost zero at long times,
at temperatures where the replica exchange occurred throughout wide temperature range.
If this is the case, the average helical content can't be defined consistently.
Ca rmsd relaxed from almost zero and at all these temperatures converged to similar values,
where the peptide seems to be a random coil.
The similar results are obtained in classical md simulations.
What should be the convergence criteria in peptide replica exchange simulations?
Please let me know some reasonable criteria, unless the simulation method is wrong.
Thanks.
Seongeun
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Received on Sun Jul 08 2007 - 06:07:22 PDT
