Pull-force error

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1

GROMACS version: 2022
GROMACS modification: Yes/No

So I am doing pull-force calculation of a protein-protein complex where I have to pull the smaller protein from the larger subunit. The pullf.xvg curve seems fine to a certain extent and goes down towards zero very usually but around 40 kJ/mol it just fluctuates around and does not converge to zero. What could this mean?

I am attaching the plot as well as my pull code. Kindly help.

Screenshot 2024-11-14 152218
Screenshot 2024-11-14 152218921×708 7.92 KB

; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = chain_B
pull_group2_name = chain_A
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = Y N N
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
pull-pbc-ref-prev-step-com = yes

2

That does not look like an error. The pull force means that the groups that you are pulling are lagging behind the pull reference position. If you add pull-print-com = yes and pull-print-ref-value = yes to your mdp options you can see this in the pullx.xvg file. The reason behind this is that there is a friction when pulling a protein in water, even if the protein is small.

3

Thank you for your reply. What do you think will solve it? I mean at any point of time, the force has to become zero, right?

4

I don’t see why it will have to become 0, except if you are pulling in vacuum.

5

I had almost come to the same conclusion to be very honest but I was advised by someone to look for a possible solutions bcs according to them it always converged to zero in their case. Is there some paper or documentation I can read to have a good understanding on this?

Thank you for the help.

6

Was their molecule as large as yours? Did they pull as quickly? Have a look at Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems | Journal of Statistical Physics. What you are observing is the dissipated force.