[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

[X Rules]

 Thanks Justin. 
Here is the quoted error:

processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'
processing coordinates...
double-checking input for internal consistency...

ERROR 1 [file protein.top, line 9279]:
  ERROR: One of the box lengths is smaller than twice the cut-off length.
  Increase the box size or decrease rlist.


-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1104

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Three Little Fonzies" (Pulp Fiction)
and the mdp
; 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             = /usr/bin/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          = 5000          ; 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     = PME   ; 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)
Hope you can locate my error here!!



> Date: Wed, 17 Nov 2010 13:09:32 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error on Box Length when adding ions	(gromacs	4.5.3/Charmm27/Tip3p)
> 
> 
> 
> X Rules wrote:
> > I am having problems with grompp with my system.
> > 
> > I am using Gromacs 4.5.3
> > FF  = Charmm27 beta
> > WT = TIP3P (recommended and its claimed its not too different than 
> > Charmms TIP3P)
> > 
> > during minimization with pbc, I get the error about box length being 
> > small if I add neutralizing ions (I do not get this error in just 
> > water+protein system).
> > 
> 
> Providing your actual sequence of commands, .mdp file(s), and the actual 
> (quoted) error message is the only way to diagnose what's going on.
> 
> > Also I have tried increasing my box length upto a cube of 40 Angstroms 
> > and still get the error ( I have a tiny 50 residue protein).
> > 
> > IS IT A BUG or I am doing something wrong.
> > 
> 
> You're probably doing something wrong, but it's impossible to say what.  Please 
> provide more detail.
> 
> -Justin
> 
> > 
> > I can add more information if needed.
> > 
> > Thanks,
> > 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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