Dear all gromacs Users! I want to run a simulation with the system protein-ligand (I have several ligands). With EM, nvt, npt step I put position restraint for the ligands and all thing was fine. After that, I run production simulation without position restraint of ligands. I saw the ligand move out of the initial position and simulation was stopped.
Did the LINCS warning happen because this system is not stable ? How can I keep the continuous running simulation without the LINCS warnings? I want the ligands are free to move and find their binding sites. This is the warnings: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem Thank you so much for any suggestions Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
