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
-------------------------------------------------------
Well, you're being given a pretty explicit hint. This is a very useful error
message. You're system is blowing up. I'd point to the relevant wiki site, but
it appears that oldwiki.gromacs.org is not operating...
In any case, better minimization and/or equilibration is necessary, as mdrun has
told you.
-Justin
; 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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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