[gmx-users] Problem of lincs in free energy calculations

[Sadaf Rani]

Dear Gromacs users
During free energy calculation, I am getting lincs warning at MD run in
some of Lambda windows. To cope with this I have reduced my time step to 1
fs rather than 2. Some of them converged but for others, it still gives
lincs warning and generates different PDB structures. If the initial
topology had some issue it should not work for any system.
Could you please suggest me how should I fix this error?

Thanks

Sadaf Rani
Ph.D. visiting student
Lancaster University
United kingdom