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: jalem...@vt.edu
> To: gmx-users@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
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
