Re: merging abf trajectories with different number of colvars

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Jun 21 2018 - 11:22:26 CDT

Souvik, thanks a lot, this is very helpful!

Olga

On Thu, Jun 21, 2018 at 11:05 AM Souvik Sinha <souvik.sinha893_at_gmail.com>
wrote:

> Hi,
>
> The 3rd and 4th column in your *.grad are the projected gradients along
> your respective reactions coordinates (i.e. your colvars) which you would
> eventually integrate to get your 2D PMF using abf_integrate routine. You
> can use this 2D landscape to get your 1D Projection of the PMF along any of
> the colvars of your choice. I think that is what Jerome meant in his
> reply.
>
> There are many literature where such an approach has been taken to
> integrate multidimensional energy landscape to get 1D PMF along a specific
> RC. If you are looking for just the equation, you can have a look at this "
> https://pubs.acs.org/doi/abs/10.1021/ct5002076".
>
> Regards,
> Souvik
>
> On Thu, Jun 21, 2018 at 7:49 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
>> Hi Jerome,
>>
>> thank you, I understand and trying my best, this list is my only source
>> to discuss technical questions at this moment.
>>
>> My two main questions are 1) what is the difference between column 3 and
>> column 4 in the *.grad output file produced after running abf with two
>> colvars (I did not find a description in the manual for the output format
>> for more than one colvar - I am not sure whether I interpret it correctly).
>>
>> and 2) whether abf_integrate routine can be used in this case (according
>> to the manual - yes, but you haven't mentioned it in your first reply and
>> started to doubt).
>>
>> I apologize for too many questions.
>>
>> Olga
>>
>>
>> On Thu, Jun 21, 2018 at 6:21 AM Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> wrote:
>>
>>> Hi,
>>>
>>> This is a fundamental question on the theory, not the software. I can't
>>> do a stat mech class on this mailing list. I can recommend Dan Zuckerman's
>>> "Statistical Physics of Biomolecules: An Introduction".
>>>
>>> Best,
>>> Jerome
>>>
>>> On 20 June 2018 at 20:18, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>
>>>> Hi Jerome,
>>>>
>>>> thank you for your answer. I am still stuck on the same problem.
>>>>
>>>> Do I understand it correctly that essentially I have to manually
>>>> extract the data and make a 1d data file (in the same format as *.pmf
>>>> produced with one colvar) in order to merge them with the rest of my
>>>> windows? Should I use abf_integrate (is that what you mean by "integrating
>>>> conditional PMFs"?) and then add this data to the plot produced by merging
>>>> the rest of the windows? Or should I extract the data from original *.grad
>>>> and *.count files without using abf_integrate routine?
>>>>
>>>> I have two colvars, distance and distanceXY.
>>>>
>>>> I tried utilizing abf_integrate program (it works and produces *.dev
>>>> *.est *.histo and *.pmf files), but I don't understand how to interpret the
>>>> output in the resulting *.pmf file and how to extract the data to combine
>>>> with with the rest of my plot.
>>>>
>>>> For example, here is a partial output from my *.pmf file (from
>>>> abf_integrate):
>>>>
>>>> 64.05 0.05 0
>>>> 64.05 0.15 1.065
>>>> 64.05 0.25 0.97875
>>>> 64.05 0.35 1.26875
>>>> 64.05 0.45 1.10063
>>>> 64.05 0.55 1.24812
>>>> 64.05 0.65 1.36687
>>>> 64.05 0.75 1.62375
>>>> ....
>>>> ....
>>>>
>>>> 64.15 0.05 0.29125
>>>> 64.15 0.15 1.26688
>>>> 64.15 0.25 1.205
>>>> 64.15 0.35 1.39375
>>>> 64.15 0.45 1.47813
>>>> 64.15 0.55 1.69625
>>>> ....
>>>> ....
>>>>
>>>> ...and so on until the first column reaches 70 (which defines the upper
>>>> border of the "distance" in my abf window). The second column, as I
>>>> understand, represents the values for "distanceXY" (0-4). The third column
>>>> is free energy, correct? Then -- how do I choose one value that corresponds
>>>> to a particular point of the distance colvar for 1D profile? (i.e. what is
>>>> the value of PMF that corresponds to, say, 64.05)
>>>>
>>>> If I don't have to use abf_integrate and take the data from original
>>>> *.grad and *.count files, how do I pick the values in the .grad file?
>>>>
>>>> My grad file looks approximately like this:
>>>>
>>>> 64.05 0.05 2.63212 18.2997
>>>> 64.05 0.15 1.53358 0.88108
>>>> 64.05 0.25 1.19012 5.24787
>>>> 64.05 0.35 1.51466 -0.261045
>>>> ...
>>>> (and so on)
>>>>
>>>> I don't quite understand what are the last two columns and how to pick
>>>> the right values there.
>>>>
>>>> I would like to understand this process and would really appreciate
>>>> help!
>>>>
>>>> Thank you,
>>>>
>>>> olga
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Mon, Jun 4, 2018 at 8:22 AM Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>>> wrote:
>>>>
>>>>> Hi Olga,
>>>>>
>>>>> The only thing ABF/colvars does is merge data for the same set of
>>>>> variables. If you ran ABF in 1d in one case, and 2d in the other
>>>>> case, you cannot merge them into a 2d PMF by any simple method. What you
>>>>> can do is "marginalize" the 2d dataset to obtain a 1d pmf that can be
>>>>> merged with the other one, but that would have to be done manually.
>>>>> Essentially that means integrating "conditional PMFs" over one variable,
>>>>> then using that as weights to compute the free energy gadient in the other
>>>>> direction as a conditional average.
>>>>>
>>>>> Best,
>>>>> Jerome
>>>>>
>>>>> On 31 May 2018 at 18:13, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I am trying to merge data from ABF runs, I have several trajectories
>>>>>> with distance colvar only and several with distance+distanceXY. I am
>>>>>> getting the following error:
>>>>>>
>>>>>> colvars: Reading sample count from abf2.count and gradient from
>>>>>> abf2.grad
>>>>>> colvars: Warning: reading from different grid definition (colvar
>>>>>> 1); remapping data$
>>>>>> colvars: Warning: reading from different grid definition (colvar
>>>>>> 1); remapping data$
>>>>>> colvars: Reading sample count from abf3.count and gradient from
>>>>>> abf3.grad
>>>>>> colvars: Error reading grid: wrong number of collective variables.
>>>>>> FATAL ERROR: Error in the collective variables module: exiting.
>>>>>>
>>>>>> What is the best way to put PMF curve together in such case? Should I
>>>>>> just extract the data columns that I need or is there a modification to
>>>>>> make in merge input files that would account for different number of
>>>>>> colvars?
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> olga
>>>>>>
>>>>>>
>>>>>
>>>
>
>
> --
> Souvik Sinha
> Research Fellow
> Bioinformatics Centre
> Bose Institute, India
>
> Contact: 033 25693275
>

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