[gmx-users] triclinic box too skewed

[Tsjerk Wassenaar]

Hi Gitta,

It may very well be that your box does not comply to the rules for a 
triclinic box in Gromacs
(p. 12 of the Manual).

The solution to the problem in that case is to:

1.) Rotate the box and the contents and
2.) Perform a lattice reduction.

I have written a perl script which gives the reoriented box vectors and 
a rotation matrix which can be used to reorient the atoms to fit in the 
new box.

The file needs the old box vectors as arguments:
./boxmtx.pl  x1  y1  z1  x2  y2  z2  x3  y3  z3

Hope it works.

Cheers,

Tsjerk


B. Nick wrote:

>Dear all,
>
>I want to run a simulation on a polyamide 
>crystal structure to test some force field
>parameter changes. The crystal unit cell 
>angles are alpha=48.5, beta=77, and gamma=63.5.
>If I try to start any simulation with this
>triclinic system I always get the error: 
>Triclinic box is too skewed.
>Does anybody know a way to solve this problem?
>
>Thanks for any help,
>Gitta
>
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