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

[Mark Abraham]

Hi,

"  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."

seems pretty specific to me. This has nothing to do with adding ions.
Setting box sizes is covered in introductory tutorials, if you need help
with that.

Mark

On Wed, Jun 1, 2016 at 7:00 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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>