Re: merging abf trajectories with different number of colvars

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Jun 21 2018 - 09:19:17 CDT

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
>>>>
>>>>
>>>
>

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