it's not clear what you mean when you say the 36 replicas are "converged".
how exactly did you determine this? also, have you looked at the
temperature sampling of the replicas? do all replicas move between all
temperatures, or are those 8 at higher T than the others? it's possible to
have a gap in sampling across a phase transition and have replicas above
and below exchanging well, but not between the 2 sets.
===================================================================
Carlos Simmerling, Ph.D.
Professor, Department of Chemistry
Associate Director, Laufer Center for Physical and Quantitative Biology
Laufer Center, Room 119 Phone: 1-631-632-5424
Stony Brook University E-mail:
carlos.simmerling.stonybrook.edu <carlos.simmerling.gmail.com>
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
===================================================================
On Fri, Apr 26, 2013 at 9:14 AM, gargi borgohai <gargib2011.gmail.com>wrote:
> Dear AMBER Users,
>
> Your suggestion regarding checking of convergence of REMD was quite
> helpful. But still one more confusion arises for confirmatrion of
> convergence. The system I am simulating has total 44 number of replicas.
> While checking convergence (RMSD plot) it is observed that out of 44
> replicas 8 replicas are showing much more fluctuations in comparision to
> the rest. The remaining 36 replicas can be concluded to be converged. Now
> my question is: do I have to run the system further so that the remaining
> replicas also get converged ?
>
> Thanking You...
> Sincerely
> Gargi Borgohain.
> PhD Scholar.
> Indian Institute of Technology, Guwahati.
> India
>
>
>
>
>
>
> Message: 15
> Date: Wed, 6 Feb 2013 07:32:35 -0500
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] Query about checking of convergence in REMD
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGk3s-SQFhMbJWM0dngkX4vSR1+_=
> X0_5cuFYE0zOkcLcZyNyw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> you can do a few things:
> - perform 2 runs, one starting from all replicas folded and 1 starting from
> all replicas unfolded. All measures should match between the 2 runs.
> anything that doesn't match is unreliable.
> - do analysis on each replica (not each temperature) separately. Every
> replica should have the same properties (rmsd histograms, fraction folded,
> fraction of time at each temperature, and so on). If they don't, it's not
> converged.
>
> remember that "converged" is a bit vague since different properties
> converge at different rates. Potential energy converges quickly, while
> structure sampling does not. Every thing you measure needs error bars. Then
> you know the precision, which is much more quantitative than a binary idea
> of "converged" or not.
>
> On Wed, Feb 6, 2013 at 7:21 AM, gargi borgohai <gargib2011.gmail.com>
> wrote:
>
> > Dear AMBER users,
> >
> > I am using REMD method to study protein folding/unfolding behavior. I
> have
> > run the system for 35ns. Can anyone help me regarding how can I confirm
> > whether my system has converged or not?
> >
> >
> > Thanking You..
> > Sincerely
> > Gargi Borgohain.
> > PhD Scholar.
> > Indian Institute of Technology, Guwahati.
> > India.
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>
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Received on Fri Apr 26 2013 - 06:30:04 PDT
