[gmx-users] question about running grompp

[nanyu101]

Hi,
  Every time when I run grompp to popc_b4em.gro,the system told me as below.But when I run grompp to speptide.gro, the result is fine.There are no such comments.I did create my grompp.mdp file by this.
touch grompp.mdp
grompp
mv mdout.mdp grompp.mdp
 And then, I did some change in grompp.mdp as I need.But the system always told me like below.



creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
' for variable comm-mode, using 'Linear'
Next time use one of: 'Linear' 'Angular' 'None'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable pbc, using 'xyz'
Next time use one of: 'xyz' 'no'
' for variable domain-decomposition, using 'no'
Next time use one of: 'no' 'yes'
' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User'
' for variable vdw-type, using 'Cut-off'
Next time use one of: 'Cut-off' 'Switch' 'Shift' 'User'
' for variable DispCorr, using 'No'
Next time use one of: 'No' 'EnerPres' 'Ener'
' for variable ewald_geometry, using '3d'
Next time use one of: '3d' '3dc'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes'
' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
' for variable Pcoupltype, using 'Isotropic'
Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic' 'Surface-Tension'
' for variable annealing, using 'no'
Next time use one of: 'no' 'yes'
' for variable gen-vel, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
' for variable constraint-algorithm, using 'Lincs'
Next time use one of: 'Lincs' 'Shake'
' for variable unconstrained-start, using 'no'
Next time use one of: 'no' 'yes'
' for variable Shake-SOR, using 'no'
Next time use one of: 'no' 'yes'
' for variable morse, using 'no'
Next time use one of: 'no' 'yes'
' for variable disre, using 'No'
Next time use one of: 'No' 'Simple' 'Ensemble'
' for variable disre-weighting, using 'Conservative'
Next time use one of: 'Conservative' 'Equal'
' for variable disre-mixed, using 'no'
Next time use one of: 'no' 'yes'
' for variable orire, using 'no'
Next time use one of: 'no' 'yes'
' for variable free-energy, using 'no'
Next time use one of: 'no' 'yes'
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
...ling /lib/cpp
: No such file or directory
cpp exit code: 32512
 popc.top > grompp2w5pfW're/top -DPOSRExp
' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file (popc_b4em.gro, 204786)
             does not match topology (popc.top, 0)


At last,the system told me the coordinates didn't match each other.Would someone like to tell me what wrong is, top file or mdp file?

Thanks a lot.Any detailed information is recommended.

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