[gmx-users] convergence of PMF

[Peter Kroon]

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?

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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>>
>>
>