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

[Justin A. Lemkul]

X Rules wrote:
> 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!!
> 

The error would imply that the box you have set up is < 2.0 nm, given the 
cutoffs here.  How did you define the box (editconf command)?  What is your box 
size (last line of the .gro file or in the header of a .pdb)?

-Justin

> 
> 
>  > 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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-- 
========================================

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

========================================