**From:** Olya Kravchenko (*ovkrav_at_gmail.com*)

**Date:** Thu Jun 21 2018 - 11:22:26 CDT

**Next message:**McGuire, Kelly: "Colvars Restraint Question"**Previous message:**Souvik Sinha: "Re: merging abf trajectories with different number of colvars"**In reply to:**Souvik Sinha: "Re: merging abf trajectories with different number of colvars"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
*

*>
*

**Next message:**McGuire, Kelly: "Colvars Restraint Question"**Previous message:**Souvik Sinha: "Re: merging abf trajectories with different number of colvars"**In reply to:**Souvik Sinha: "Re: merging abf trajectories with different number of colvars"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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