From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 29 2016 - 10:14:34 CST
Hi Bala,
On Tue, Nov 29, 2016 at 10:39 AM, Bala subramanian <
bala.biophysics_at_gmail.com> wrote:
> Friends,
> My aim is the following, a) Study the pmf of a single potassium ion
> through a channel, b) Study the pmf of a single potassium ion in the
> presence of additional ion. The objective is to calculate the force (along
> the reaction coordinate) on my testing ion in the absence and presence of
> additional ion, and also the PMF profile.
>
You mean like in this 2001 paper?
http://www.nature.com/nature/journal/v414/n6859/abs/414073a0.html
and the many others that were published in the past two decades?
> colvarsTrajFrequency 500
> colvarsRestartFrequency 500
> colvar {
> name Translocation
> width 0.2
> lowerboundary -4.0
> upperboundary -1.0
> lowerwallconstant 20.0
> upperwallconstant 20.0
> distanceZ {
> main {atomnumbers { 16625 } # My testing ion
> ref { atomnumbers { 2025 7565 13105 }
> }
> axis ( 0.0, 0.0, 1.0 ) }
> }
>
> colvar {
> name Additional
> width 0.2
> lowerboundary -9.0
> upperboundary -7.0
> hardLowerBoundary yes
> hardUpperBoundary yes
> lowerwallconstant 20.0
> upperwallconstant 20.0
> distanceZ {
> main { atomnumbers { 16624 } # additional ion from my testing ion
> }
> ref { atomnumbers { 16625 }
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
>
> abf {
>
> colvars Translocatio
>
> fullSamples 800
>
> historyFreq 500
>
> }
>
> a) Which is the correct colvar option that I should choose to obtain the
> correct force on my testing ion *OutputTotalForce* or *oneSiteTotalForce*
>
The two are not interchangeable, outputTotalForce is (as the name says)
only an output flag, which does not change the dynamics. oneSiteTotalForce
means that out of multiple sites, only one will be used for the total force
calculation. You only have one site anyway (one atom, even) so that flag
doesn't change anything.
> b) I am using latest namd version, the manual says that there is a
> *subtractAppliedForce* option available, but it is not recommended.
>
Well, it is definitely not recommended to use it if you don't know for sure
what it does.
Can you try a second read of the manual, and also of the following page?
https://colvars.github.io/totalforce.html
As illustration for everybody, subtractAppliedForce would not change the
dynamics on the setup you posted. There is no applied force other than the
ABF one, which will be subtracted internally to the ABF bias anyway before
printing the PMF. The wall forces *will* appear in the total force, but
won't be counted in the PMF because they are outside the boundaries.
If you had e.g. a constant harmonic potential on the *same* variable, the
subtractAppliedForce flag would allow you to remove such potential from the
PMF. I'd recommend, however, not to do that, for the reasons explained in
the webpage above and the manual.
If you had a non-constant potential applied to the variable, or any other
non-constant external force, you shouldn't run ABF in the first place
because it would never converge.
Unfortunately the issue is highly dependent of your system setup, so it's
not possible to simplify it further.
> There is also *ouputAppliedforce* option. Should i simply obtain the
> totalfoce and subtract the appliedforce to remove any force due to bias ?
>
You can do that a posteriori, of course, if you know the applied force.
> Could you please guide which options should I use to achieve my objective.
>
>
> --
> C. Balasubramanian
>
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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