[gmx-users] How to solve the "LINCS WARNING" problem

[Yu Du]

Hi Jinyoung,

You made it clear.

If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand.

To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy.

Could you run the following simulation to pinpoint the error?

(1) Simulation only all-atom ligand in the system.
(2) Simulation only protein in the system.
(3) Simulation only united-atom ligand in the system if it's possible.

In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation.

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Cheers,
Yu