[gmx-users] problem with energy minimization

[sanjay23 at iitb.ac.in]

dear gromacs user
i am doing simulation of Gal1p protein with ligand and without ligand.i
made the system without ligand by removing the ligand from pdb file then i
use pdb2gmx for generating topology file and editconf for adding box
dimention and add spc water molecules.i have not face any problem up to
grompp but when i did energy minimization of system i got this warning:-
"Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is
larger than the 1-4 table size 1.000 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"
but em is comleted with machine precession with -ve energy,  i added
table-extention (1.1nm)in mdp file, and got same warning.even i don't what
affect done on system by adding table-extention.I am also getting same
problem  with ligand.kidnely help me
sanjay

itle               =   Gal1p
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt                  =  0.002    ; ps !
nsteps              =  50000
nstlist             =  10
nstcomm             =  1
nstxout             =  1000
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.1
;
;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.01