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AMBER Archive (2007)Subject: AMBER: Convergence criteria in replica exchange simulations
From: Seongeun Yang (seongeun_at_korea.ac.kr)
Hello experts,
I have done replica exchange simulations for two alanine-based polypeptides,
The number of replicas are 40 and 46 for each case.
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,
I have some questions on the convergence criteria in replica exchange simulations,
The helical contents are severely fluctuating as expected,
Ca rmsd relaxed from almost zero and at all these temperatures converged to similar values,
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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