convergence of abf

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Fri Sep 12 2008 - 10:03:17 CDT

Hi Eric Lee,

Thanks for your reply - I have another peptide where the sampling is not
uniform. Would one than sample the areas which were not sampled as much and
than average against the main simulation - like if you have made a 5 ns
simulation and from 15 to 17 the sample size is very small so I would than
make a new simulation from 15 to 17 and combine the results with the "old"
simulation. But when you combine should it be a weighted average - A = 10
for 10.000 and A = 4 for 90.000 ?

Thanks in advance

Best regards

J

On Mon, Sep 8, 2008 at 9:45 PM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:

> 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
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:17 CST