[gmx-users] convergence of PMF

[abhisek Mondal]

Hi,

Thank you for the comments. That was really helpful.

On Fri, Nov 17, 2017 at 7:22 PM, Peter Kroon <p.c.kroon at rug.nl> wrote:

>
>
> On 17-11-17 14:48, Justin Lemkul wrote:
> >
> >
> > On 11/17/17 8:47 AM, Peter Kroon wrote:
> >>
> >> On 17-11-17 14:38, Justin Lemkul wrote:
> >>>
> >>> On 11/17/17 6:28 AM, abhisek Mondal wrote:
> >>>> 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 ?
> >>> No, because you're conducting a non-equilibrium process, which is not
> >>> going to give you a PMF.
> >>>
> >>> Your system is changing over time due to the application of a biasing
> >>> potential. It does not make sense to say that anything there converged
> >>> based on any time-dependent quantity.
> >> But shouldn't you be able to look at the force-vs-time profiles of your
> >> windows? So that you can at least say that the force per window is
> >> equilibrated?
> >
> > The OP mentioned a PMF, which is equilibrium sampling and indeed you
> > *could* look at those forces, but then in this post it is mentioned
> > that it's a non-equilibrium SMD simulation (non-zero pull rate), so
> > no, there's nothing useful to look at here.
> >
> > I would also just bypass the forces anyway, since they are extremely
> > noisy, and compute the PMF over different windows of time. That's the
> > most straightforward way to look at convergence (and what reviewers
> > *always* ask to see in papers).
> Cheers, thanks for your insight.
>
> Peter
> >
> > -Justin
> >
> >> Peter
> >>
> >>> -Justin
> >>>
> >>>>
> >>>> 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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> >>
> >>
> >>
> >
>
>
>
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-- 
Abhisek Mondal

*Senior Research Fellow*

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

*Kolkata 700032*

*INDIA*