[gmx-users] Inconsistent shifts - is it something wrong with pbc

ming ma morning22704 at gmail.com
Tue Mar 6 20:54:02 CET 2012


Thanks for looking at this email. Before I asked this question, I have read
most of the related topics in gromacs's mailing list, but still can't solve
When I was trying to do energy minimization of graphene with pbc, I got
several messages "there are # inconsistent shifts, check your topolgy."
After the mimization is finished, the energy in extremely large (1.86e+05
kJ/mol), which is obviously wrong. To make sure that I haven't done any
stupid mistake, I have carried out energy minimization of the same system
using LAMMPS, and the results is reasonable (the energy is -205.14 eV). The
configuration of the system has also been checked by visualizing it in VMD,
and the PBC seems right.

Below is my mdp file,

; energy minimization
integrator               = l-bfgs
nsteps                   = 5000
constraints              = none
emtol                    = 1.0
nstcgsteep               = 10 ; do a steep every 10 steps of cg
emstep                   = 0.01 ; used with steep
nbfgscorr                = 10
nstcomm                  = 0 ; frequecy of remove of com movement
Tcoupl                   = no
Pcoupl                   = no

; potential and neigbor related
coulombtype              = Cut-off
rcoulomb                 = 1.2
vdw-type                 = Switch
rvdw-switch              = 0.8
rvdw                     = 1.0
; neighbor list related
rlist                    = 1.2
nstlist                  = 10
ns_type                  = grid

pbc                      = xyz
;output section
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 100
nstenergy                = 100
nstxtcout                = 0
xtc_precision            = 1000
xtc-grps                 =
energygrps               =

And these are parts of the message I got during simulation,

There were 262 inconsistent shifts. Check your topology
Will stop reporting inconsistent shifts

This is the results I got
Low-Memory BFGS Minimizer converged to Fmax < 1 in 432 steps
Potential Energy  =  1.85767014488657e+05

I also tried using the cg method instead of l-bfgs, after read the log
files carefully, I found these messages,

Initializing Domain Decomposition on 4 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
    two-body bonded interactions: 14.880 nm, Morse, atoms 8401 8540
  multi-body bonded interactions: 20.914 nm, G96Angle, atoms 8470 8540
Minimum cell size due to bonded interactions: 23.006 nm

I checked the distances between the atoms it showed, obviously, this large
distance is caused by not having taken the pbc xyz into consideration since
the size of the simulation box is 15*15**6 nm. So does it mean I haven't
handle the pbc correctly? Since I notice in the message posted before some
of the 'inconsistent shifts' are also caused by pbc problems.

Thanks for your kind help

Dr. Ming MA
Department of  Chemistry, University College London
London Centre for Nanotechnology
17-19 Gordon Street
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