Re: ABF: umbrella_int.awk

From: yjcoshc_at_gmail.com
Date: Sat Jul 15 2017 - 07:02:33 CDT

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 <mailto: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 <mailto:giacomo.fiorin_at_gmail.com>> wrote:
>
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-110003.3
> <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 <mailto: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 <mailto: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 <mailto: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
> <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 <https://github.com/giacomofiorin>
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:26 CST