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
--
========================================
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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