<br>Hi<br>In the system, one lysozyme + TIP3P water.<br><br>After the two commands,<br>grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr <br>mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR <br><br><br><br>
<br>pr.mdp, minim.mdp and the error information is as follows.<br>nsteps = 5000 ; Maximum number of (minimization) steps <br>How to solve the problem?<br><br>Thank you<br>Lin<br><br><br><br>-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 4.0.5<br>Source code file: domdec.c, line: 3651<br><br>Fatal error:<br>A charge group moved too far between two domain decomposition steps<br>This usually means that your system is not well equilibrated<br>
-------------------------------------------------------<br><br><br><br><br><br>; VARIOUS PREPROCESSING OPTIONS<br>title = <br>cpp = /lib/cpp<br>include = <br>define = -DPOSRES<br>
<br>; RUN CONTROL PARAMETERS<br>integrator = md<br>tinit = 0<br>dt = 0.001<br>nsteps = 5000<br>nstcomm = 0<br><br>; OUTPUT CONTROL OPTIONS<br>
nstxout = 0<br>nstvout = 0<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 1<br>nstxtcout = 0<br>xtc_precision = 1000<br>
xtc-grps = System<br>energygrps = Protein Non-Protein<br><br>; NEIGHBORSEARCHING PARAMETERS<br>nstlist = 5<br>ns-type = Grid<br>pbc = xyz<br>
rlist = 0.9<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>coulombtype = Reaction-Field<br>rcoulomb = 1.4<br>epsilon_rf = 78<br>epsilon_r = 1<br>
vdw-type = Cut-off<br>rvdw = 1.4<br><br>; Temperature coupling <br>Tcoupl = Berendsen<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>
ref_t = 200 200<br><br>; Pressure coupling <br>Pcoupl = No<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = yes<br>gen_temp = 200.0<br>
gen_seed = 1735<br><br>; OPTIONS FOR BONDS <br>constraints = all-bonds<br>constraint-algorithm = Lincs<br>unconstrained-start = no<br>lincs-order = 4<br>lincs-iter = 1<br>
lincs-warnangle = 30<br><br><br><br><br><br><br>; LINES STARTING WITH ';' ARE COMMENTS<br>title = Minimization of Lysozyme (1LW9.pdb) ; Title of run<br><br>; The following lines tell the program the standard locations where to find cert<br>
ain files<br>cpp = /lib/cpp ; Preprocessor<br><br>; Definea can be used to control processes<br>define = -DFLEXIBLE<br><br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimizati<br>
on)<br>emtol = 1.0 ; Stop minimization when the maximum force < 1.0<br> kJ/mol<br>nsteps = 5000 ; Maximum number of (minimization) steps to perf<br>orm<br>nstenergy = 1 ; Write energies to disk every nstenergy steps<br>
energygrps = System ; Which energy group(s) to write to disk<br><br>; Parameters describing how to find the neighbors of each atom and how to calcul<br>ate the <br>interactions<br>nstlist = 5 ; Frequency to update the neighbor list and long<br>
range forces<br>ns_type = simple ; Method to determine neighbor list (simple, gri<br>d)<br>rlist = 1.0 ; Cut-off for making neighbor list (short range <br>forces)<br>coulombtype = cut-off ; Treatment of long range electrostatic interact<br>
ions<br>rcoulomb = 1.0 ; long range electrostatic cut-off<br>rvdw = 1.0 ; long range Van der Waals cut-off<br>constraints = none ; Bond types to replace by constraints<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br><br><br><br>