[gmx-users] convergence of PMF

[Justin Lemkul]

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.

-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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>
>

-- 
==================================================

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

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