Chih-Ying Lin wrote:
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
-------------------------------------------------------
I haven't seen much of this error, but it seems akin to the usual
"blowing up" symptoms one gets when a starting structure is
poorly-conditioned with respect to its physics. This generates large
forces and velocities, and something breaks. Here, some charge group has
moved too far.
You need to look carefully at your structures and see what, if anything,
looks wrong. If this error occurred after few integration steps (see the
.log file) then your starting structure has a problem. Try a vacuum
simulation, or solvating differently. Without knowing how you've
prepared the system, it's impossible to give concrete advice.
Mark
; 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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