<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 &#39;;&#39; 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 &lt; 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>