nitu sharma wrote:
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,
Have a look here:
http://oldwiki.gromacs.org/index.php/blowing_up
-Justin
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= 479
-------------------------------------------------------
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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--
========================================
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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