Re: inputPrefix merge error ABF

From: Giacomo Fiorin (
Date: Tue Apr 02 2019 - 12:02:25 CDT

FYI as Jeff explained by default NAMD will switch its working directory to
the parent directory of the given configuration file, regardless of where
it's being called from.

However, you can use *namd2 --source <path_to_config_file>* to just read
the config file, but not switch to that file's parent directory. This
should allow you to read the configuration from a file anywhere on the file
system, but keep working in the same directory where you launch NAMD.


On Tue, Apr 2, 2019 at 12:05 PM Jeff Comer <> wrote:

> Dear Abhi,
> The new .hist.grad files and .hist.count files are a continuation of
> the evolution of the ABF bias, in the same way that the DCD files are
> a continuation of the trajectory of the coordinates. Your new DCD is
> initially smaller than the previous DCD file. Your new .hist.grad and
> .hist.count files are analogously smaller than the previous .hist.grad
> and .hist.count files.
> All of the information necessary for the current and future
> application of the ABF method are included in the count (.count) and
> gradient (.grad) files. The count is the number of samples in each bin
> along the reaction coordinate and the gradient is the mean force on
> the reaction coordinate for each of these bins. When you use
> inputPrefix, ABF uses these count and gradient files to set the
> initial state and starts accumulating new samples from there.
> Internally, the Colvars code stores a "count" grid and a "sum of force
> samples" grid (count_i * gradient_i). The entire history of force
> samples at each step (ξ_s, F(ξ_s)) is not stored, nor is the history
> of the evolution of the count and gradient grids stored (except if you
> specify a historyFreq and write the .hist.count and .hist.grad files).
> As I see it, the .hist.grad and .hist.count files are only useful for
> convergence analysis and statistical analysis of your free energy
> calculation.
> I hope that helps to clarify what is going on.
> Regards,
> Jeff
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website:
> On Mon, Apr 1, 2019 at 10:29 PM Abhishek TYAGI <>
> wrote:
> >
> > Dear Jeff,
> >
> >
> > Thanks for the reply and your suggestion worked perfectly when I put
> *.count and *.grad files in the same folder as of namd conf file.
> >
> >
> > I have a stupid question, I am not sure why this is happening:
> >
> > The new data obtained for pmf, hist.pmf hist.grad .. etc, have numbers
> inside, however, I noticed that the file size is far smaller than the
> earlier files from the same MD, as I have used inputprefixto combine them--000000000000274cca05858f1c50--

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