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>
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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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Received on Fri Apr 26 2013 - 06:30:02 PDT
