[gmx-users] convergence of PMF

[abhisek Mondal]

Hello,

I understand the invariant trend is the key feature to look out for in this
case.

But, is it possible to comment on the convergence from Force-vs-Time plot ?
I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
pulling the force became zero and thus the biasing potential goes also to
zero. Hence, after 5 nm of dissociation the PMF should attain convergence
if also invariant trend-line is found near that point.

Does this explanation make any sense from convergence of PMF's perspective ?



On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> One way to get some degree of confidence is to use the bootstrapping/error
> analysis options provided in gmx wham. But Justin is right you are looking
> for time invariance. So: use the first portion of your trajectory (say
> first 60%) and compute the PMF, then use the first 65% of your trajectory
> and see if it has changed (and by how much), then 70%, and 80% and so on.
> If you have converged (within reason), you should see that at some point,
> as you add more time to the analysis the PMF doesn't change (in any
> statistically significant way), when that occurs you have "converged".
>
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: Thursday, November 16, 2017 8:04 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] convergence of PMF
>
> On 11/16/17 3:34 AM, abhisek Mondal wrote:
> > Hi,
> >
> >      I have derived a PMF (protein-ligand) using umbrella sampling
> method.
> > But how can I comment if the obtained PMF has converged well ? What are
> the
> > ways to check the convergence of a PMF ?
>
> How would you check convergence of any quantity? You have to determine
> if the result is changing over time, and if it is invariant (within the
> context of available statistics), then the quantity is converged.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*