[gmx-users] convergence of PMF

[Peter Kroon]

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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>>>>
>>
>>
>>
>