From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jul 15 2017 - 03:36:33 CDT
Thanks for all information.However, I dare saying that there also
biochemists here, like myself, who have a limited background in biophysics
but would like to compare theory with their experiments. I believe I
understand the reasons for the said deconvolution, and what "Krestr =
extended system force constant" stands for. Nonetheless I am unable to
carry out such a deconvolution (even for the example in the 2017 tutorial,
not only for my system) because I find no access to Krestr.
It would help:
(1) Knowing whether all settings in the 2017 protein-tutorial for ABF
Conformation Bound are such as the Krestr value should appear at the
beginning of the colvars output file (which does not, as far as I could
investigate). If setting are not enough, which other definition of colvars
should be implemented in order to get that Krestr.
(2) Should that above not work, is that too much asking for the explicit
expression mentioned in "recalculate it yourself - the expression is given
in the user's guide" of previous mail along this thread?
I sincerely beg pardon for posing questions on matter that apparently has
no mystery for other guys on this forum.
thanks
francesco
On Fri, Jul 14, 2017 at 3:21 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Note also that at the beginning of the User's Guide is a table of
> contents, with links.
>
> On Fri, Jul 14, 2017 at 9:20 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> http://colvars.github.io/colvars-refman-namd/colvars-refman-
>> namd.html#x1-110003.3
>>
>> On Fri, Jul 14, 2017 at 4:39 AM, Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> 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?
>>>
>>> Thanks
>>> francesco
>>>
>>> On Thu, Jul 13, 2017 at 8:14 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>> 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 <chiendarret_at_gmail.com>
>>>> 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
>>>>>
>>>>
>>>>
>>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> 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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