[gmx-users] Error during minimization

[nishap.patel at utoronto.ca]

I have a question regarding the simulations that I am running. I tried  
creating a pdb file with one methane and water molecules, but the  
system keeps showing 'bad contact' error when I run the minimization  
step and I don't understand what I am doing wrong.

  This is my methane file :

TITLE     methane  in water
CRYST1   33.010   33.010   33.010  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  CH4 CH4     1      19.520  25.090  16.410  1.00  0.00

So I use this file and run editconf -f methane1.pdb -o box.pdb -bt  
cubic. This creates a
box with volume of around 35 nm^3

Then I add water molecules using :

genbox -cp box.pdb -cs spc216 -o methwa.pdb -p topol.top

This adds around 1191 water molecules to the existing methane file. So  
my box is now
(33.010 33.010 33.010 with total 1192 molecules). Then I run  
minimization on this system
using minim.mdp as follows:

integrator        = steep
emtol                = 1.0
nsteps                = 100
nstenergy        = 10
nstxtcout        = 10
xtc_grps        = CH4 SOL
energygrps        = CH4 SOL
nstlist                = 5
ns_type                = simple
rlist                = 1.0
coulombtype        = cut-off
rcoulomb        = 1.0
rvdw                = 1.0
constraints        = none
pbc                = no

grompp -f minim.mdp -c methwa.pdb -p topol.top -v
  mdrun -v

And it runs minimization with bad contact errors and this is the result I get:
Steepest Descents converged to machine precision in 32 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -4.9481789e+04
Maximum force     =  3.2827865e+06 on atom 500
Norm of force     =  6.9951227e+04


Any suggestions?

Nisha.P