[gmx-users] I want to drag two atoms together with GROMCS SMD options.

[Vytautas Rakeviius]

Hello,
I want to drag two atoms together with GROMCS SMD options.But I tried different options and still those groups are pushed away one from another.I would be very thankful if someone edits this code example (from: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp) in such way that Chan_A and Chain_B comes together into covalent bounding rage or similar:; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_B
pull_group2_name        = Chain_A
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0