[gmx-users] gromacs doubt

[manjula kasinathan]

hi all

       i have done protein protein interaction and the complex structure
  was taken for MD simulation using Gromacs.while performing mdrun step for
position restrain i got error. i have carried out mdrun for 1ps and the
command given for mdrun
  and position restrain are
        grompp -f *.pdb -c *.gro -p top.top -o *.tpr
        mdrun -v -deffnm pr
my em.mdp file

title                   = com
cpp                     = /usr/local/gromacs/share/gromacs/cpp ; the c
pre-processor
define                  = -DFLEXIBLE
constraints             = none
integrator              = steep
dt                      = 0.002    ; ps !
nsteps                  = 3000
nstlist                 = 10
ns_type                 = grid
rlist                   = 1.0
coulombtype             = PME
rcoulomb                = 1.0
vdwtype                 = cut-off
rvdw                    = 1.4
fourierspacing          = 0.12
fourier_nx              = 0
fourier_ny              = 0
fourier_nz              = 0
pme_order               = 4
ewald_rtol              = 1e-5
optimize_fft            = yes
;
;            Energy minimizing stuff
;
emtol                   = 1000.0
emstep                  = 0.01.

here i have given nsteps 3000. but while doing energy minimization it
considers only 1000 steps and the energy was minimized for only 1000 steps.
then i gone for position restrain step while doing Mdrun i got error like
this

starting mdrun 'Protein in water'
500 steps,      1.0 ps.
step 400, remaining runtime:   132 s
Step 402, time 0.804 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000119, max 0.006712 (between atoms 2873 and 2875)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2873   2875   64.4    0.0989   0.1007      0.1000

t = 0.868 ps: Water molecule starting at atom 93766 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

wat should i do now. how can i progress this.could any one help me plz.
thank in advance

Cheers,
Manjula Kasinathan.
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