On 4/19/13 2:25 PM, Nuria Cirauqui Diaz wrote:
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
layers?
grompp only issues that error based on box vectors and cutoffs. It has nothing
to do with the fact that some amino acids are not bathed in solvent. There must
be some problem with box vectors somewhere, but we don't have nearly enough
information to assess that based on what you've posted.
-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
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