[gmx-users] question

[s.ghasemlou]

Hello every one, 

After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
topol.top -o ions.tpr" I get the error: 

ERROR 1 [file topol.top, line 863]:
  ERROR: The cut-off length is longer than half the shortest box vector
or
  longer than the smallest box diagonal element. Increase the box size
or
  decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343) 

I have tried different rlist, r columb and rvdw values. I have also
changed the box vector several times, but I still get the same error. I
don't know how to change them to fix the error. 

There is also the below warning:

Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
- OW)
Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
HW1)
Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
- HW2)
Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
- OW)
Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
HW1)
Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
- HW2)
Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
- OW)
Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
- HW1)
Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
- HW2)
Warning: atom name 10 in topol.top and totalbox1.gro does not match
(H110 - OW)
Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
- HW1)
Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
- HW2)
Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
- OW)
Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
- HW1)
Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
- HW2)
Warning: atom name 16 in topol.top and totalbox1.gro does not match
(H100 - OW)
Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
- HW1)
Warning: atom name 18 in topol.top and totalbox1.gro does not match
(H102 - HW2)
Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
- OW)
Warning: atom name 20 in topol.top and totalbox1.gro does not match
(H101 - HW1)
(more than 20 non-matching atom names) 
WARNING 1 [file topol.top, line 863]:
  32798 non-matching atom names
  atom names from topol.top will be used
  atom names from totalbox1.gro will be ignored 

As I checked both the .gro and topol.top contents, atom names are the
same but here atom names of solvent water are mixed with atom names of
the ligand I used. 
please help me on this. Thanks in advance.