Re: merging abf trajectories with different number of colvars

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jun 04 2018 - 07:22:34 CDT

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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