Re: Inconsistent PMF profile of Ionized polymer

From: Jérôme Hénin (
Date: Mon Jan 17 2022 - 12:28:48 CST

Hi Victor,

----- On 14 Jan 22, at 18:44, Victor Hue <> wrote:

> Dear all,

> I'm using colvars module in LAMMPS, but I believe I will get more help from here
> for enhanced sampling module.

This is a little irregular, but your questions are relevant to the NAMD community as well, so it's fine with me.

> I have 2 questions:

> Question 1

> I have been using umbrella sampling methods for the free energy analysis of
> polymer adsorption from a solid surface. Below are some of the US simulation
> details:

> Distance from the polymer COM to the solids surface: 16A,
> Total window stages: 81 windows
> Window spacing interval: 0.2A between successive windows
> Equilibration time for each window: 6ns (Total all windows 486ns)
> Force constant: 100 kcal/mol.A^2 (after rescale with width 0.1)

> harmonic {
> name h_pot
> colvars dist
> forceConstant 1
> centers {different window stage centre}
> writeTISamples
> outputCenters yes # Write the current centers to the trajectory file
> }

> Using a post trajectory processing tool (WHAM analysis tool by Grossfield), I'm
> able to produce a reasonable PMF profile. However, with different initial
> starting position of the polymer, the PMF profile produced can be quite
> different. Therefore, 10 runs of different initial position are repeated and to
> be averaged for a single polymer case and the results are included in the
> document in the link. The 2 different figures are for the same type of polymer,
> but in neutral and ionized form.

> [
> |
> ]

> It is clear that the neutral polymer has a more consistent PMF profile while the
> ionized polymer can be very inconsistent. I wonder what is the reason causing
> the ionized polymer to have so different range of PMF value? To elaborate more,
> sodium ions are put in the ionized polymer cases to ensure electroneutrality.
> The run 1-5 has smaller PMF value (sodium ions are put near to polymer), while
> run 6-10 seems to have deeper PMF value (sodium ions are put near to solid
> surface).

> I wonder is that because of sodium ions, or any simulation details can I change
> to improve and make it more consistent?

I suspect that the ions are responsible for this. The interactions of a charged polymer with the surface will depend on the position of the counter-ions, and those with fluctuate slowly, introducing noise in your measurements. One option is to increase the ion concentration to improve the sampling. In any case, you should monitor the ion-polymer interactions.

> Question 2

> With the built-in US method in colvars module, ( targetNumSteps and
> targetNumStages ), the PMF profile can be produced from the command writeTIPMF
> . However, is the PMF produced the true PMF, or it contains the biased
> potential? Asking this because I try to change a force constant value from 100
> to 200 kcal/mol.A^2. As a quick analysis (1ns simulation), the PMF profile from
> the command has no difference for a simpler single water molecule, but the PMF
> profile produced is deeper for the polymer with higher force constant.

Could this be a non-equilibrium effect? What happens if you pull slower? (or faster)


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