# PULL simulation while forcing groups to be parallel **URL:** \ **Category:** User discussions\ **Created:** [June 22, 2020, 11:39pm UTC](https://gromacs.bioexcel.eu/t/pull-simulation-while-forcing-groups-to-be-parallel/361 "2020-06-22T23:39:07Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Mikel](https://avatars.discourse-cdn.com/v4/letter/m/e480ec/32.png) [@Mikel](https://gromacs.bioexcel.eu/u/Mikel)\ **Post date:** [June 22, 2020, 11:39pm UTC](https://gromacs.bioexcel.eu/t/pull-simulation-while-forcing-groups-to-be-parallel/361/1 "2020-06-22T23:39:08Z")
GROMACS version: 2020.1 GROMACS modification: No Greetings, 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? Kind regards and thank you for your time ---
**Author:** ![Aparna1](https://avatars.discourse-cdn.com/v4/letter/a/b5ac83/32.png) [@Aparna1](https://gromacs.bioexcel.eu/u/Aparna1)\ **Post date:** [July 14, 2024, 2:25pm UTC](https://gromacs.bioexcel.eu/t/pull-simulation-while-forcing-groups-to-be-parallel/361/2 "2024-07-14T14:25:36Z")
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.