Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error.
Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) 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 ------------------------------------------------------- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? I would like some help on the matter Jocley
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