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

[Justin Lemkul]

On 11/13/12 3:20 AM, sri2201 wrote:
> Dear All ,
>
> 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
-- 
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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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