Re: ABF: umbrella_int.awk

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Jul 15 2017 - 08:45:00 CDT

Thanks from francesco

On Sat, Jul 15, 2017 at 2:02 PM, <yjcoshc_at_gmail.com> wrote:

> Hi,
>
> As far as I know, you can calculate the krestr or spring force constant
> like this:
>
> 1. Find the boltzmann constant in kcal/(mol*k), let it be kb;
>
> 2. Find the temperature running with your simulation, let it be T;
>
> 3. Find the extendedFluctuation value you have set in your colvars input
> file, let it be sigma;
>
> krestr = kb*T/(sigma*sigma)
>
> This formula is in the NAMD user guide. You can do a global search("spring
> force constant") in the PDF version user guide to find it.
>
> 在 2017年07月15日 16:36, Francesco Pietra 写道:
>
> 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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