gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr

Fatal error:

number of coordinates in coordinate file (solv_ions.gro, 63371)does not match topology (topol.top, 63831).

other error:

gmx mdrun -v -deffnm em

Running on 1 node with total 4 cores, 8 logical cores

Hardware detected:

CPU info:

Vendor: GenuineIntel

Brand: Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz

SIMD instructions most likely to fit this hardware: AVX2_256

SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this machine, which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)

Using 1 MPI thread

Using 8 OpenMP threads

Steepest Descents:

Tolerance (Fmax) = 1.00000e+00

Number of steps = 200

WARNING: Listed nonbonded interaction between particles 5785 and 5793

at distance 4.605 which is larger than the table limit 2.050 nm.

This is likely either a 1,4 interaction, or a listed interaction inside

a smaller molecule you are decoupling during a free energy calculation.

Since interactions at distances beyond the table cannot be computed,

they are skipped until they are inside the table limit again. You will

only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is

probably something wrong with your system. Only change the table-extension

distance in the mdp file if you are really sure that is the reason.

Step= 0, Dmax= 1.0e-02 nm, Epot= 8.76758e+08 Fmax= 7.64933e+08, atom= 5793

Step= 1, Dmax= 1.0e-02 nm, Epot= 8.61484e+08 Fmax= 7.54645e+08, atom= 5793

Step= 2, Dmax= 1.2e-02 nm, Epot= 8.43425e+08 Fmax= 7.42439e+08, atom= 5793

Step= 3, Dmax= 1.4e-02 nm, Epot= 8.22138e+08 Fmax= 7.27917e+08, atom= 5793

Step= 4, Dmax= 1.7e-02 nm, Epot= 7.97140e+08 Fmax= 7.10775e+08, atom= 5793

Step= 5, Dmax= 2.1e-02 nm, Epot= 7.67914e+08 Fmax= 6.90564e+08, atom= 5793

Step= 6, Dmax= 2.5e-02 nm, Epot= 7.33935e+08 Fmax= 6.66818e+08, atom= 5793

Step= 7, Dmax= 3.0e-02 nm, Epot= 6.94697e+08 Fmax= 6.39042e+08, atom= 5793

Step= 8, Dmax= 3.6e-02 nm, Epot= 6.49759e+08 Fmax= 6.06729e+08, atom= 5793

Step= 9, Dmax= 4.3e-02 nm, Epot= 5.98824e+08 Fmax= 5.69388e+08, atom= 5793

Step= 10, Dmax= 5.2e-02 nm, Epot= 5.41835e+08 Fmax= 5.26548e+08, atom= 5793

Step= 11, Dmax= 6.2e-02 nm, Epot= 4.79153e+08 Fmax= 4.77895e+08, atom= 5792

Step= 13, Dmax= 3.7e-02 nm, Epot= 4.45785e+08 Fmax= 4.50293e+08, atom= 5792

Step= 14, Dmax= 4.5e-02 nm, Epot= 4.24034e+08 Fmax= 1.32019e+09, atom= 5793

Step= 15, Dmax= 5.3e-02 nm, Epot= 4.20527e+08 Fmax= 4.31300e+08, atom= 5793

Step= 16, Dmax= 6.4e-02 nm, Epot= 3.67714e+08 Fmax= 3.86114e+08, atom= 5792

Step= 17, Dmax= 7.7e-02 nm, Epot= 3.15804e+08 Fmax= 5.07046e+08, atom= 5793

Step= 18, Dmax= 9.2e-02 nm, Epot= 2.75895e+08 Fmax= 3.07168e+08, atom= 5793

Step= 19, Dmax= 1.1e-01 nm, Epot= 2.14119e+08 Fmax= 2.47945e+08, atom= 5793

Step= 20, Dmax= 1.3e-01 nm, Epot= 1.56000e+08 Fmax= 1.87026e+08, atom= 5793

Step= 21, Dmax= 1.6e-01 nm, Epot= 1.18647e+08 Fmax= 1.43850e+09, atom= 5793

Wrote pdb files with previous and current coordinates

-------------------------------------------------------

Program gmx mdrun, VERSION 5.1.2

Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 22: Water molecule starting at atom 12828 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

please reply.