AMBER Archive (2007)

Subject: Re: AMBER: Convergence criteria in replica exchange simulations

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 05 2007 - 07:26:26 CDT

try looking at these, all have pretty extensive examples of checking
REMD convergence.

Wickstrom, L., Bi, Y., Hornak, V., Raleigh, D. and Simmerling, C.,
"Reconciling the Solution and X-ray Structures of the Villin Headpiece
Helical Subdomain: Molecular Dynamics Simulations and Double Mutant
Cycles Reveal a Stabilizing Cation-Pi Interaction", Biochemistry,
46:3624-3634 (2007) (listed as "Hot Article" by Biochemistry)

Roe, D., Okur, A., Wickstrom, L., Hornak, V. and Simmerling, C.,
"Secondary Structure Bias in Generalized Born Solvent Models:
Comparison of Conformational Ensembles and Free Energy of Solvent
Polarization from Explicit and Implicit Solvation", J. Phys. Chem. B,
111:1846-1857 (2007)

Okur, A., Roe, D., Cui, G., Hornak, V. and Simmerling, C., "Improving
Convergence of Replica Exchange Simulations through Coupling to a High
Temperature Structure Reservoir", J. Chem. Theory & Comput., 3:557-568
(2007)

On 7/5/07, Seongeun Yang <seongeun_at_korea.ac.kr> wrote:
> 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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