I need to perform non-equilibrium simulation to push DNA through a channel such that it also revolves within the channel. The final goal is to conduct umbrella sampling simulation to calculate PMF of DNA motion (revolution+translocation). I tried 2D pulling using distance (push in z axis) and angle (revolve in channel) parameters, but the angle parameter is not revolving DNA properly and only works up to 180 degree. I also tried transformation pull coordinate but did not succeed in getting the required helical motion.
Could you please inform me how I can do this in gromacs?
Could you provide the parameters you were using in the mdp file, the commands you used and any messages that were output onto the terminal (warnings, notes, errors, etc)? Visualizing the system and providing a snapshot might also be helpful
I used non-equilibrium simulation to revolve and translocate the DNA along the channel using the following gmx script. BUT I’m unable to calculate the PMF profile afterwards as gmx WHAM only reads the pull files (pull=yes) and not the rotation files (obtained via enforced rotation=yes).
; ENFORCED ROTATION
rotation = yes ; yes
rot_ngroups = 1
rot_group0 = DNA
rot_type0 = pm
rot_massw0 = no
rot_vec0 = 0 0 1
rot_pivot0 = 7.67706 7.70904 12.24
rot_rate0 = 1.75
rot_k0 = 1000
rot_fit_method0 = potential
rot-nstrout=100
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = DNA
pull_group2_name = VAZ ; virtual particle that will apply pushes on each center of mass of base pair
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ;
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.012 ; = 0.1 0.1 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Could you please let me know how to use gmx wham to calculate PMF from enforced rotation output files.