[gmx-users] Problem with minimizing the energy of the solvated system

[Justin A. Lemkul]

On 7/5/12 3:15 PM, jonas87 wrote:

Chopping out a bunch of unnecessary stuff...

> *editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
> 1.0 *
>
> Read 1202 atoms
> No velocities found
>      system size :  5.245  4.320  2.507 (nm)
>      diameter    :  5.532               (nm)
>      center      :  0.010  0.047 -0.011 (nm)
>      box vectors :  0.000  0.000  0.000 (nm)
>      box angles  :   0.00   0.00   0.00 (degrees)
>      box volume  :   0.00               (nm^3)
>      shift       :  5.640  5.602  2.674 (nm)
> new center      :  5.649  5.649  2.663 (nm)
> new box vectors :  7.532  7.532  7.532 (nm)

Here, you're setting the box.  The dimensions look sensible.

(Chopping out more extraneous stuff)

Here's where something is going wrong.  Without seeing the contents of 
minim.mdp, it's hard to say exactly what, aside from a generic comment that the 
settings in the .mdp file are incompatible with the size of the box.  Typically 
tutorials work quite well, so you should ensure that you're following everything 
exactly and keeping track of all your files so nothing has gotten switched up.

> grompp -v -f minim.mdp -c protein-solvated.pdb -p protein.top -o
> protein-EM-solvated.tpr *
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> processing topology...
> Generated 141 of the 1176 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
> Excluding 1 bonded neighbours molecule type 'CL'
> processing coordinates...
> double-checking input for internal consistency...
>
> ERROR 1 [file protein.top, line 7583]:
>    ERROR: One of the box lengths is smaller than twice the cut-off length.
>    Increase the box size or decrease rlist.
>
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
> 1372
>
> 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
> -------------------------------------------------------
>

Did you follow the link?  It's where you can find an answer to almost every 
error you'll encounter.  For instance:

http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist

-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

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