[gmx-users] cut-off length error

Mahmood Naderan nt_mahmood at yahoo.com
Fri Feb 23 19:04:02 CET 2018


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
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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
[ 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

[ system ]

[ 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?


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