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

[Mark Abraham]

The text of the error has nothing to do with the ions you may or may not
need to add. Please read more closely.

Mark

On Wed, 1 Jun 2016 06:57 kamakshi sikka <kamakshi.sikka at gmail.com> wrote:

> 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
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