[gmx-users] Re: error : One of the box lengths is smaller than twice the cut-off length
jalemkul at vt.edu
Tue Nov 13 15:09:34 CET 2012
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.
> 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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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