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. <smit...@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-boun...@maillist.sys.kth.se < >>>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of >>>>> Justin >>>>> Lemkul <jalem...@vt.edu> >>>>> Sent: Thursday, November 16, 2017 8:04 AM >>>>> To: gmx-us...@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 >>>>> >>>>> jalem...@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-requ...@gromacs.org. >>>>> >>>>> -- >>>>> 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-requ...@gromacs.org. >>>>> >>>> >> >> >> >
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