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

[Justin Lemkul]

On 11/13/12 9:05 AM, Dr. Vitaly Chaban wrote:
>>> 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.
>

rlist defaults to 1.0 nm, per the manual.  More problematic in this case is the 
lack of nstlist, which defaults to 10, but should be set to 1 for EM.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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