[gmx-users] Re: error : One of the box lengths is smaller than twice the cut-off length

[Dr. Vitaly Chaban]

>> I am getting following error while trying the energy minimization  by using
>> following command
>>
>> gromacs-4.5.5/proj1% grompp -v -f minim.mdp -c protein-solvated.pdb -p
>> protein.top -o protein-EM-solvated.tpr
>>
>> *ERROR 1 [file protein.top, line 6486]:*
>>    ERROR: One of the box lengths is smaller than twice the cut-off length.
>> Increase the box size or decrease rlist.
>>
>> *
>> mdp file information *
>>
>> ; Lines starting with ';' ARE COMMENTS
>> ; Everything following ';' is also comment
>>
>> title         = Energy Minimization   ; Title of run
>>
>> ; The following line tell the program the standard locations where to find
>> certain files
>> cpp           = /lib/cpp      ; Preprocessor
>>
>> ; Define can be used to control processes
>> define          = -DFLEXIBLE
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator    = steep         ; Algorithm (steep = steepest descent minimization)
>> emtol         = 1.0           ; Stop minimization when the maximum force < 1.0 kJ/mol
>> nsteps                = 500           ; Maximum number of (minimization) steps to perform
>> nstenergy     = 1             ; Write energies to disk every nstenergy steps
>> energygrps    = System        ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> ns_type               = simple        ; Method to determine neighbor list (simple, grid)
>> coulombtype   = cut-off       ; Treatment of long range electrostatic interactions
>> rcoulomb      = 1.0           ; long range electrostatic cut-off
>> rvdw          = 1.0           ; long range Van der Waals cut-off
>> constraints   = none          ; Bond types to replace by constraints
>> pbc           = xyz           ; Periodic Boundary Conditions (yes/no)
>>
>> please suggest needful
>>
>
> Your box is too small.
>
> http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
>
> -Justin


Your box is not just small, it is ridiculously small.

Also, you have no RLIST keyword in your MDP file. I do not how GROMACS
behaves in this situation, but you anyway need to set RLIST
explicitly, since it can add problems and instability to your
simulations.


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark