**From:** zeynab hosseini (*hosseinizeynab93_at_gmail.com*)

**Date:** Tue Sep 01 2020 - 12:52:30 CDT

**Next message:**zeynab hosseini: "toppar_water_ions.str NAMD format for last version of C36 (on July 2020)"**Previous message:**Jérôme Hénin: "Re: ABF Not Sampling Whole Window"**In reply to:**Giacomo Fiorin: "Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances..."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Giacomo,

I have spend almost a lot of time to go through the journal articles to

understand what you were explained to me and I forgot to thank you for the

comprehensive answer. It indeed was true and worked for me. Thanks you so

much..

On Thu, Apr 16, 2020 at 10:36 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

wrote:

*> Hi Zeynab, one small correction. I just noticed that you are using
*

*> distanceXY, i.e. the distance in cylindrical rather than polar
*

*> coordinates. The Jacobian term of the PMF in that case would be just -kB T
*

*> ln(r).
*

*>
*

*> Giacomo
*

*>
*

*> On Thu, Apr 16, 2020 at 10:13 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
*

*> wrote:
*

*>
*

*>> Hi Zeynab, this is possibly due to the Jacobian term of the PMF, which
*

*>> comes from the geometric definition of the variable. See e.g. the
*

*>> appendices of the Colvars paper:
*

*>> https://doi.org/10.1080/00268976.2013.813594
*

*>> For a distance "r" there are increasingly more microscopic states as you
*

*>> go to a larger r, because every spherical shell between r and (r + dr)
*

*>> carries a number of angular states proportional to 4 pi r^2. The Jacobian
*

*>> term for a distance can be calculated to be -kBT ln(r^2), or -2 kBT ln(r).
*

*>>
*

*>> This term is physically correct: for exactly one amino acid molecule and
*

*>> one nanotube in a macroscopic sample, one the amino acid leaves it will
*

*>> never find its way back, as there is simply too much volume for it to
*

*>> explore. You may think of this as an entropic term to the PMF.
*

*>>
*

*>> The reason why you expect the PMF to flatten out is because PMFs are
*

*>> often computed from a g(r), which is computed for a finite concentration of
*

*>> both species (amino acid and nanotube). So even if one amino acid molecule
*

*>> leaves for good, there are others ready to take its place to compensate.
*

*>>
*

*>> Try adding 2 kB T ln(r) to your plots and see if the PMF flattens.
*

*>>
*

*>> Giacomo
*

*>>
*

*>> On Thu, Apr 16, 2020 at 12:17 AM zeynab hosseini <
*

*>> hosseinizeynab93_at_gmail.com> wrote:
*

*>>
*

*>>> Dear All,
*

*>>>
*

*>>> I'm new in the umbrella sampling (US) method. I followed the NAMD
*

*>>> tutorial performing US technique to calculate the adsorption free energy of
*

*>>> an amino acid (AA) on (infinite) single-walled carbon nanotube (SWCNT)
*

*>>> surface. I used the weighted histogram analysis method (WHAM) to
*

*>>> reconstruct the potential of mean force (PMF) from biased potential. The
*

*>>> point is that we expect the pmf flatten when the AA distance from the CNT
*

*>>> increases. But, as it is seen in the attached plot, the pmf reduces when
*

*>>> the AA is getting close to the simulation box edges (around 30A). I wonder
*

*>>> why this reduction happens. I reviewed namd-l following all related
*

*>>> suggestions. Moreover, I plotted pmf every 6ns and I need help to
*

*>>> conclude whether the pmf is converging. The windows overlap is good... I
*

*>>> also attached the colvars input file (US-base.in) and configuration file
*

*>>> (win-base.conf) if it is conjectured something is wrong with them...
*

*>>>
*

*>>> The CNT is fixed at the center of the 60A *60A *30A simulation box of
*

*>>> water molecules and oriented along the z-axis. The reaction coordinate is
*

*>>> the radial distance of the AA from the center of the CNT. The bounds of the
*

*>>> reaction coordinate are 6.8A and 27.8A and the windows are spaced 1A apart,
*

*>>> centered at 6.8A, 7.8A...27.8A. Each window is sampled for 38ns. The force
*

*>>> constant is 2.5kcal/mol.
*

*>>>
*

*>>> Would be thankful if anybody guides me.
*

*>>> All the best,
*

*>>> Zeynab
*

*>>>
*

*>>
*

*>>
*

*>> --
*

*>> Giacomo Fiorin
*

*>> Associate Professor of Research, Temple University, Philadelphia, PA
*

*>> Research collaborator, National Institutes of Health, Bethesda, MD
*

*>> http://goo.gl/Q3TBQU
*

*>> https://github.com/giacomofiorin
*

*>>
*

*>
*

*>
*

*> --
*

*> Giacomo Fiorin
*

*> Associate Professor of Research, Temple University, Philadelphia, PA
*

*> Research collaborator, National Institutes of Health, Bethesda, MD
*

*> http://goo.gl/Q3TBQU
*

*> https://github.com/giacomofiorin
*

*>
*

**Next message:**zeynab hosseini: "toppar_water_ions.str NAMD format for last version of C36 (on July 2020)"**Previous message:**Jérôme Hénin: "Re: ABF Not Sampling Whole Window"**In reply to:**Giacomo Fiorin: "Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances..."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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