[gmx-users] problem in energy minimisation of dna-protein complex

nitu sharma sharmanitu35 at gmail.com
Thu Jul 2 13:30:14 CEST 2009

Dear all

                I am doing simulation of dna -protein complex . in this
processing I am getting error in energy minimisation step-

the error comes like this-
There were 2 inconsistent shifts. Check your topology
There were 4 inconsistent shifts. Check your topology
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =        10000
There were 6 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 1 and 6 at distance 7.731 which is larger
than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
There were 6 inconsistent shifts. Check your topology=         inf, atom=

Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 10648 ]


My em.mdp file is like this-
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt                  = 0.001
nsteps              =  10000
;       Energy minimizing stuff
emtol               =  100
emstep              =  0.01

nstcomm             =  1
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
vdw-type            = cut-off
rvdw                =  1.0
coulombtype         =  PME
Tcoupl              =  no
Pcoupl              =  no

gen_vel             =  no
comm-mode           = Linear
pbc                 = XYZ

can anyone suggest how can i get rid from this problem.
Thanks a lot in advance.
Nitu sharma
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