Re: merging abf trajectories with different number of colvars

From: Olya Kravchenko (
Date: Wed Jun 20 2018 - 13:18:11 CDT

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

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,


On Mon, Jun 4, 2018 at 8:22 AM Jérôme Hénin <> 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 <> 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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:11 CST