[gmx-users] cut-off length error

[Justin Lemkul]

On 2/23/18 1:03 PM, Mahmood Naderan wrote:
> Hi,
>
> I downloaded a water benchmark from gromacs web site
> and tried to run a sample. However it fails with a cut-off
> length error while there is no such parameter in topol.top
>
>
>
> mahmood at orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/0000.65$ ls
> conf.gro  mdout.mdp  pme.mdp  rf.mdp  topol.top
> mahmood at orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/0000.65$ gmx grompp -f pme.mdp -c conf.gro -p topol.top -o wa.tpr
>                         :-) GROMACS - gmx grompp, 2018 (-:
>
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>   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
>      Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
>    Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff
>     Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
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>
> GROMACS:      gmx grompp, version 2018
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/mahmood/gromacs-2018/bench/water-cut1.0_GMX50_bare/0000.65
> Command line:
>    gmx grompp -f pme.mdp -c conf.gro -p topol.top -o wa.tpr
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
> Setting the LD random seed to 2025508713
> Generated 330891 of the 330891 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 330891 of the 330891 1-4 parameter combinations
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
>
> ERROR 1 [file topol.top, line 37]:
>    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
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)
>
> 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
> -------------------------------------------------------
> mahmood at orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/0000.65$ cat topol.top
> #include "oplsaa.ff/forcefield.itp"
> [ moleculetype ]
> ; molname    nrexcl
> SOL        2
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>       1  opls_116   1    SOL     OW      1      -0.8476
>       2  opls_117   1    SOL    HW1      2       0.4238
>       3  opls_117   1    SOL    HW2      3       0.4238
>
> #ifndef FLEXIBLE
> [ settles ]
> ; OW    funct    doh    dhh
> 1    1    0.1    0.16330
>
> [ exclusions ]
> 1    2    3
> 2    1    3
> 3    1    2
> #else
> [ bonds ]
> ; i    j    funct    length    force.c.
> 1    2    1    0.1    345000    0.1     345000
> 1    3    1    0.1    345000    0.1     345000
>      
> [ angles ]
> ; i    j    k    funct    angle    force.c.
> 2    1    3    1    109.47    383    109.47    383
> #endif
>
> [ system ]
> Water
>
> [ molecules ]
> SOL    216
>
>
>
>
>
>
>
>
> I am not a researcher in this field. I just want to run
> some test as a system admin.
>
> The topol.top has 37 lines and the last line (after SOL)
> is just an enter! What should I do?

The interaction cutoff length is a component of the physical model and 
therefore determines a minimum system size. You need to build a larger 
simulation system to satisfy this requirement.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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