Fwd: convergence of abf

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Mon Sep 08 2008 - 14:45:53 CDT

Begin forwarded message:

> From: "Eric H. Lee" <ericlee_at_ks.uiuc.edu>
> Date: September 8, 2008 2:45:31 PM CDT
> To: Jorgen Simonsen <jorgen589_at_gmail.com>
> Subject: Re: namd-l: convergence of abf
>
> At 5ns and 100,000 sample size, thats essentially your reaction
> coordinate split into 50 sampling windows. If there are any
> distinct barriers encountered along the way (essentially a sudden
> rise in the PMF), you may wish to sample that event a little bit
> longer. However the uniform distribution spread over your entire
> sampling time is a pretty good indication of convergence.
>
> -Eric
>
> On Sep 8, 2008, at 9:16 AM, Jorgen Simonsen wrote:
>
>> Hi all,
>>
>> I have performed a ABF simulation where I am trying to stretch a
>> peptide - the samples are more or less uniform distributed where
>> the sample size is around 100.000 but how can one be sure that the
>> energy has converged? My sampling time 5 ns which is a ilttle short
>> but.....
>>
>> Any advice or comments appreciated
>>
>> thanks in advance
>>
>> Best
>> J
>
> Eric H. Lee
> Medical Scholars Program
> Theoretical and Computational Biophysics Group, UIUC
> ericlee_at_ks.uiuc.edu
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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