ming ma wrote:
Hi,
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 it.
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.
Exactly, the periodicity is not being handled correctly. Presumably you're
dealing with an infinite sheet (thus bonds extend across periodic boundaries),
and thus you need to set "periodic_molecules = yes" in the .mdp file.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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