[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)

[Arunima Shilpi]

Sir
I am studying protein-ligand interaction through umbrella sampling. I used
the following value foe md_pull.mdp file

pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = Y Y Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = prc
pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2

and box size details is

editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12

while runnimg the command for

mdrun -s pull.tpr

Have the following error

"Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the
box size (2.184750)"

I request you to kindly help me to debug the error




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Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha