[gmx-users] Cut off problem with protein in water-vacuum-water layers

Nuria Cirauqui Diaz ncirauqu at gmail.com
Fri Apr 19 20:25:05 CEST 2013

Hi all,

I am trying to run a simulation of a protein in a water-vacuum-water box,
which simulates quite well the membrane environment. I did it some years
ago in amber, but know I am trying in grommacs and got the following answer
when I try to run the fist "mdp" file:

ERROR: 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 rvdw.

Of course, I tried to use the same water box complete (no deleting the
vacuum layer), and it run well. So, it is not a problem of the size, but of
the fact of having some aminoacids not surrounded by water. There is any
option of changing some parameter in the "mdp" file (cut-off scheme...) to
avoid this problem, still keeping my protein in the water-vacuum-water


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