[gmx-users] Error while generating ions.tpr file

[kamakshi sikka]

Hello,

I am doing mixed lipid bilayer simulation with a peptide. This bilayer
membranewas built by Charmm Gui. Afterwards, I oriented the peptide on the
top of the bilayer and then saved the peptide+membrane complex file. Then ,
I am trying to add ions into the system by giving the command mentioned
below.But, this is giving an error. This membrane already has  'SOD'
ions in it. Is it creating a problem while adding CL ions into the system?
Please help.

*COMMAND:*
gmx grompp -f ions.mdp -c complex_new.pdb -p topol.top -o ions.tpr


NOTE 1 [file ions.mdp, line 17]:
  ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
  Probably it was first intended for use with GROMACS before 4.6. In 4.6,
  the Verlet scheme was introduced, but the group scheme was still the
  default. The default is now the Verlet scheme, so you will observe
  different behaviour.


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#

NOTE 2 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2538245621
Generated 73900 of the 73920 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 47534 of the 73920 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'POPS'
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'SOD'

NOTE 3 [file topol.top, line 2253]:
  System has non-zero total charge: 5.000001
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.




ERROR 1 [file topol.top, line 2253]:
  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.


Removing all charge groups because cutoff-scheme=Verlet

There were 3 notes

-------------------------------------------------------
Program gmx, VERSION 5.0.2
Source code file:
/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/grompp.c, line: 1723

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Regards
Kamakshi Sikka