[gmx-users] convergence of PMF

[Smith, Micholas D.]

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

==================================================

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.