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)




------------------------------------------------------------------------

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
========================================

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

========================================
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to