[gmx-users] Help with pull code for umbrella pulling

[Slabbert, B, Mr [bslabbert@sun.ac.za]]

Hi,

I am currently trying to perform an umbrella simulation on a nucleosome structure. I am trying to pull the C-terminal tail away from the rest of the structure.

I am at the pulling stage  and run:

gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -r npt.gro -o pull.tpr
gmx mdrun -s pull.tpr

However, after this upon inspecting the COM distance profile, the centre of masses don't move away from each other as intended. They jag closer and further away from one another.
Bellow follows the pullcode:

; Pull code
pull                    = yes
pull_ncoords            = 1
pull_ngroups            = 2
pull_group1_name        = Chain_A
pull_group2_name        = Chain_B
pull_group1_pbcatom     = 22197
pull_group2_pbcatom     = 22223
pull_coord1_type        = umbrella
pull_coord1_geometry    = distance
pull_coord1_dim         = N N Y
pull_coord1_groups      = 1 2
pull_pbc_ref_prev_step_com = yes
pull_coord1_start       = yes
pull_coord1_rate        = 0.008
pull_coord1_k           = 1000

I created index groups for the C chain of the structure. Chain_A is the tail that I want to pull away from the main structure Chain_B. I want to pull in the z-direction.
I also added positional constraints to Chain_B.

I presume that the pulled groups are not correctly specified, because when I look at the conf.gro files after this step there is hardly any movement in the structure.

Any insight would be greatly appreciated.

Kind regards,
Benilo Slabbert
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