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

[Justin Lemkul]

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

-- 
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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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