Force fluctuation calculation using constraint simulation in pull code?

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1

GROMACS version: 2020.1
GROMACS modification: Yes/No
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I want to calculate average constraint force for each distance and these average forces were numerically integrated to calculate the potential of mean force.
I am using pull code mdp options:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = PDMS
pull_group2_name = DMPC
pull-group1-pbcatom = 16865
pull-group2-pbcatom = 7955
pull-pbc-ref-prev-step-com = yes
pull_coord1_type = constraint ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = no ; define initial COM distance > 0
pull_coord1_init = 3.242 ; 0.01 nm per ps = 10 nm per ns
pull_nstxout = 1
pull_nstfout = 1

But this is not giving correct results.

Can someone help me to do this calculation?

2

You have not provided any information on what goes wrong, so we can not provide any help.

Is one of the two groups a membrane? If yes, then you should use pull_coord1_geometry=cylinder and umbrella sampling instead of a constraint.

3

I want to calculate constraint force fluctuations at each distance to calculate the diffusion coefficient.
I am attaching a paper related to this.
https://doi.org/10.1021/acsomega.1c04684

4

You still don’t state what goes wrong.