Re: ABF: umbrella_int.awk

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jul 14 2017 - 08:21:10 CDT

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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