[gmx-users] ERROR: box vectors is shorter than twice the cut-off

[David van der Spoel]

On Mon, 29 Dec 2003, Michele Fuortes wrote:

>Hi,
>
>I have installed gromacs-3.2.0_beta1 on a Macintosh with OS 10.3, and
>everything seemed to work well.
>No I'm trying to get the surface potential for a protein that I have
>modeled on a similar protein which has a crystal structure with
>swiss-model. The original protein file runs well.
>But if I try to run the modeled protein (with the default .mdp file
>settings) I get:
>
>ERROR: One of the box vectors is shorter than twice the cut-off length.
>Increase the box size or decrease rcoulomb.


you should do as it says, and make the box larger:

editconf -f in.gro -o out.gro -box 5 5 5 -c


>
>or if I decrease the rcoulomb
>
>ERROR: One of the box vectors is shorter than twice the cut-off length.
>Increase the box size or decrease rlist.
>
>then if I decrease the rlist I get the first error again. I am a little
>baffled because the two protein are quite similar and if I look at the pdb
>file there are same size.
>I think it could be a problem with a mis-formatted pdb file.
>Does anyone have a suggestion on what to do, or where to look. Note that I
>am quite a novice with gromacs, please be patient ;-). I searched the list
>archives but could not find an answer.
>
>
>Thanks
>
>Michele
>

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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