Rate and force unit conversion for pulling paramters

User discussions
1

Hello good people,

I need your help! I know this is very basic, but I want to cross-check if my unit conversions are correct, as I need to use these values for the following two parameters in my simulation.
I want to pull C-terminal at constant velocity of 10^5 μm/s by using a harmonic spring with the force constant of 5 × 10^4 pN/μm. Can I use it like this, if so is my conversion correct?

The default units for the parameters are:
pull-coord1-rate = [nm/ps]
pull-coord1-k = [kJ mol^-1 nm^-2]

I’m trying to convert to different units and came up with the following:

  1. 10^5 μm/s = 10^-4 nm/ps
  2. 1 pN/μm = 6.022 × 10^-11 kJ/mol/nm²
    so, 5 × 10^4 pN/μm = 3.011 × 10^-6 kJ/mol/nm²
    Codes:

; Pull code
pull = yes
pull_ngroups = 2 ; Two groups involved
pull_group1_name = group1
pull_group2_name = group2
pull-group1-pbcatom = 3750
pull-pbc-ref-prev-step-com = yes
pull_ncoords = 1 ; One coordinate for pulling

; Define pull coordinates
pull-coord1-type = umbrella ; Umbrella pulling
pull-coord1-groups = 1 2 ; 1 for reference, 2 for the atom to be pulled
pull-coord1-geometry = distance ; Distance geometry
pull-coord1-dim = N Y N ; Only consider the Y component of the distance
pull-coord1-start = yes ; Start from the initial configuration
pull-coord1-rate = ??? ; nm per ps
pull-coord1-k = ??? ; Force constant in kJ mol^-1 nm^-2 , need to use (5 × 10^4 pN/μm)

Thanks in advance!

2

Hi,
Before doing any unit conversions, please have a look at Molecular dynamics parameters (.mdp options) - GROMACS 2024.3 documentation, specifically “For constant force pulling this is the force constant of the linear potential, and thus the negative (!) of the constant force in kJ mol-1 nm-1 (or kJ mol-1 rad-1 for angles).”

I think that will save you some trouble.