GROMACS version: 5.1.1
GROMACS modification: Yes/No
I am getting LINCS warning after 200 ns of MD run. The same protein with other ligands is running properly up to 500 ns. How can I deal with this error?
I have seen suggestions like using -maxwarn to ignore the lincs warning.
But how and where to use it?
Is there any way I can move ahead with my current simulation?
Could you copy-paste the command you used, and all the messages that were output into the terminal (warnings, errors, notes, etc.)? It might also be helpful if you’re able to visualize what the system looks like and send a snapshot
Hi Karis,
Thanks for responding. I am attaching the snapshots of the files for your reference. As you can see, these steps files are generated after running for some time.
Error: (out_md)
Hi SuKriti,
Lincs warning usually mean that the system is not well equilibrated, if you have a modified molecule it could also mean that a bond is not properly defined in the topology. Using the -maxwarn option will not work beacuse it only supresses the grompp warnings and not those generated by mdrun, nonetheless, you wouldn’t want to supresss Lincs warnings as they could indicate there is something really wrong with your system. I’d advise you to try and equilibrate your system again, doing an Energy Minimization with a maximum force of 1, NVT and NPT equilibrations (I would do it for 100ps each). If nothing works, I’d try building the system again.
Ps: It seems there is nothing wrong with your mdp file