Hi The system is "one lysozyme + water " running on 16 nodes.
After => Energy minimization of the solvated systemRelaxation of solvent and hydrogen atom positions: Position restrained MDThen, the error was shown. ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated ------------------------------------------------------- The energy minimization is as follows ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 500000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk But, the above error is still there. My understanding is that "A charge group moved too far between two domain decomposition steps" comes from the bad water sampling. The bad water sampling will make the charge groups too close. The, they are against each other sharply and leave each other with a high speed. How to solve the problem ?? Thank you Lin
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