I wan to conduct the simulation of LiTFSI ionic liquid. When I run the simulation with the time step of 2 fs I face this warning:
WARNING 1 [file topol.top, line 13]: The bond in molecule-type TFSI between atoms 5 S1T and 6 O1T has an estimated oscillational period of 5.8e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option.
When I set the time step on 1fs Warning 1 changes to Note 1. How can I fix it?
If you are sure that the parameters for that bond, as well as the masses of the atoms, are correct, you would probably have to switch to constraints = all-bonds. But you should probably verify that your force field works properly with all bonds constrained. Most force fields do, but most are parametrized with only h-bonds constrained.
Thanks for your answer. My force field is OPLS-AA.
Can we conclude that some structures can be simulated only in small time steps? Polymers are usually (not always) simulated at 2 fs time steps. Whenever I could not increase the time step to 2 fs, I figured out there was a problem in my topology file. Is it correct for other structures? (For example, in TFSI salt in my case)
Also, my case is made of LiTFSI salt in polymer. How can I constraint just TFSI? Do I have to define a freezed group and add to mdp file?
Indeed, with correct topologies (parameters) you can usually use 2 fs timesteps with constraints = h-bonds. I would expect so here as well. Have you verified that the OPLS-AA parameters are correct for this bond and the involved atoms? I can’t even find what atom types O1T and S1T are supposed to represent. Are they really standard OPLS-AA atom types? Are you sure that the atom types are correctly assigned? Have you found any published work simulating these molecules with OPLS-AA?
You could see if it helps constraining this specific bond.
In the publication, they integrate with a step size of 1 fs. The note that you get with dt = 1 was added after 5.0.7, I think. So, they would probably also get that note simulating with a more recent version. The note is not as severe as the warning, so hopefully it will be fine.
