Re: ABF: umbrella_int.awk

From: Francesco Pietra (
Date: Fri Jul 14 2017 - 03:39:48 CDT

Hi Jerome:
I have now run, for comparison with my system, the 2017 ABF tutorial
protein-ligand, Conformation, Bound along 30.000 steps only. Outputs have
the same layout as for my system.

The beginning of bound-1-01_0.colvars.traj reads:

# step r Theta
Phi Psi theta
           0 2.21264748116377e+01 9.88241538497830e+01
-1.56036780260276e+01 2.81125103179902e+01 3.71653966824358e+01
-8.90756156240459e+01 1.3204510

Has Krestr to be looked for at the beginning of another file? I have
examined all at no avail.


recalculate it yourself - the expression is given in the user's guide.

could you be so kind to provide a link?


On Thu, Jul 13, 2017 at 8:14 PM, Jérôme Hénin <> wrote:

> Hi Francesco,
> The value is computed at the beginning of the simulation, based on the
> provided extendedFluctuation value. You can get it from the colvars output,
> or even recalculate it yourself - the expression is given in the user's
> guide.
> Jerome
> On 13 July 2017 at 17:32, Francesco Pietra <> wrote:
>> Hello:
>> With ABF, I am unable to catch the Krestr value to insert into
>> umbrella_int.awk.
>> From the tutorial protein-ligand "The value of Krestr is logged at the
>> beginning of the NAMD output file."
>> from the script itself :
>> # Krestr (mandatory: -v Krestr=XXX), get value from colvars output
>> # "Computed extended system force constant"
>> I must say that I have completed the "Conformation Bound" only, while the
>> "Conformation Unbound" was started and later on killed on a work station,
>> waiting for the cluster, as the system is large. Is the Krest value only
>> provided at completion of the simulation?
>> thanks
>> francesco pietra

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