[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)
xrules at live.com
Wed Nov 17 19:23:01 CET 2010
Here is the quoted error:
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'
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
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.
> > 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
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