Hi In the system, one lysozyme + TIP3P water. After the two commands, grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR
pr.mdp, minim.mdp and the error information is as follows. nsteps = 5000 ; Maximum number of (minimization) steps How to solve the problem? Thank you Lin ------------------------------------------------------- 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 ------------------------------------------------------- ; VARIOUS PREPROCESSING OPTIONS title = cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md tinit = 0 dt = 0.001 nsteps = 5000 nstcomm = 0 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10 nstenergy = 1 nstxtcout = 0 xtc_precision = 1000 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 200 200 ; Pressure coupling Pcoupl = No ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed = 1735 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of Lysozyme (1LW9.pdb) ; Title of run ; The following lines tell the program the standard locations where to find cert ain files cpp = /lib/cpp ; Preprocessor ; Definea can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimizati on) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 5000 ; Maximum number of (minimization) steps to perf orm nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calcul ate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, gri d) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interact ions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no)
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