GROMACS version:
GROMACS modification: Yes/No
I have 100 ns trajectory of a protein-protein complex. I wanted to calculate the angle between 2 chains but before that I wanted to fix 1 chain so that it is not moving but the other chain is moving. How can I do that?
You can try that with gmx trjconv. Make a group with only the chain that you want fixed and then with gmx trjconv -fit rot+trans you can fit the trajectory with respect to a certain structure. Just pick the C-alphas of the chain you want fixed, this should work well if the chain is not changing to much. You will probably need to fix pbc/make molecules whole before fitting.
Keep in mind that this won’t change the output value of the angle however!
Thank you for the response. I have done this but still i can see some movement in the protein that is fixed. I want it to be absolutely static so that the change in angle values over trajectory only comes from the movement of the chain that is moving.. Can you please explain what do u mean by “this won’t change the output value of the angle however!”
Completely fixed is impossible if the chain wobbles, which is basically always, if the chain is not a rigid rod without any other degrees of freedom. What I mean with change the angle value is that the angle is relative to the chain, so a change of frame of reference (here I mean Cartesian frame, not the frames of the MD), that is, moving the reference with one that is consistent with one chain, won’t change the angles values, is these are calculated relatively to the chains themselves.
is there a way I can completely immobilize the chain during or before the simulation?
What do you mean with before the simulation? You can immobilize it fully during the simulation by employing large restraints to the chain atoms, for example.
As mentioned in one of the comments, you can make the chain completely static during the simulation. You can do this either by applying position restraints or using colvars with a higher force constant. Gromacs also has a freeze atoms option that you can add in your topology file and then run the simulations.