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

sri2201 penumutchu.srinivas at gmail.com
Tue Nov 13 09:20:34 CET 2012

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 

Thanking you 

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