From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jul 14 2017 - 08:20:15 CDT
On Fri, Jul 14, 2017 at 4:39 AM, Francesco Pietra <chiendarret_at_gmail.com>
> 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
> phi RMSD r_RMSD
> 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 <jerome.henin_at_ibpc.fr>
>> 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
>> On 13 July 2017 at 17:32, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>> With ABF, I am unable to catch the Krestr value to insert into
>>> 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?
>>> francesco pietra
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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