Inconsistent PMF profile of Ionized polymer

From: Victor Hue (
Date: Fri Jan 14 2022 - 11:44:55 CST

Dear all,

I'm using colvars module in LAMMPS, but I believe I will get more help from
here for enhanced sampling module. 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}
  outputCenters yes # Write the current centers to the trajectory

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.;!!DZ3fjg!ucE80VxDdFKE34FKOcV0mXBgLtg0Qxj2pItCmZySYoj_mXjHH4z79pPFWIAwfGC94Q$

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?

*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.

Thank you.


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