I am comparing a number of protein unbinding PMF estimations done with Umbrella Sampling. My proteins are straight helices that associate through a hydrophobic interface. Up until now, I was using the pull code with the helices COM as reaction coordinate, which works great, but because the pull setup only takes into account the distance between the COMs, sometimes the helices rotate, or stick on one side of the other one. In order to make the different simulations more easily comparable, I would like to make the pulling procedure more standarized.
I would like to know if there is any way to ‘force’ the pulling simulation to keep both helices straight while they are being pulled apart. I have tried the cylinder pull coordinate, but it does not work quite as I wanted. I have also tried setting up two pull coordinates, one in each side of the helices, but this tends to break the helices in the middle.
Before I attempt to set up a custom collective variable with PLUMED, can anyone think of something within gromacs itself?
Hello,
I have a similar problem. I am using steered MD to pull a protein, but during the simulation the protein rotates. But I want to have the same conformation, so how can I constrain the rotation? I tried to use enforced rotation, but when I did this, my protein was not pulled. Can someone help me with this?
This is my mdp file
;enforced rotation
rotation = yes ; apply rotation potential (yes/no)
rot-ngroups = 1 ; ; number of rotation groups
rot-group0 = prot2 ; name of rotation group in the index file
rot-type0 = iso ;(iso) type of rotation protential applied to rotation group 0 (iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t)
rot-massw0 = no ; (no) use mass weighted rotation group positions
rot-vec0 = 1 0 0 ; ; rotation vector, will get normalised
rot-rate0 = 0 ; ; reference rotation rate (degree/ps) for group 0
rot-k0 = 600 ; force constance (kJ/(mol*nm^2)) for group 0
rot-fit-method0 = norm ; fetting method to determine angle of rotation group (rmsd, norm, or potential)
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = prot1
pull-group1-pbcatom = 3104 ; GLU291 calpha atom
pull_group2_name = prot2
pull-group2-pbcatom = 13504 ; GLU291 calpha atom
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1-dim = N Y N
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.00001 ; 0.00001 nm per ps = 0.1 nm per ns
pull-pbc-ref-prev-step-com = yes
pull_coord1_k = 10000 ; kJ mol^-1 nm^-2
Thanks in advance.