[gmx-users] error with cut-off length using verlet scheme in stochastic dynamics simulation

Amanda Parker asparker at ucdavis.edu
Wed Sep 28 21:12:40 CEST 2016


I am trying to run a stochastic dynamics simulation and am getting the

"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 rlist."

I've increased my box vectors to 100 nm, 100 nm, 100 nm (as I see confirmed
at the bottom of my .gro file). I am using the Verlet cut-off scheme, which
as I understand it makes rlist irrelevant and uses its own default cut-off
length (perhaps of 0.005?), unless I specify verlet-buffer-tolerance = -1.
I have tried using no verlet-buffer-tolerance line, as well as using
verlet-buffer-tolerance = -1 and setting rlist = 2. Both of these options
continue to give the error above.

How do I check the cut-off length for Verlet scheme? Without being able to
do that, I cannot confirm that the cut-off length is indeed longer than
half the shortest box vector. That said, I would be surprised if the
cut-off length was longer than 50 nm.

I'm happy to include copies of any files that you feel are necessary to
understanding this problem. At this point it seems the only information
necessary are the box vectors and cut-off length (and in this case the fact
that I'm using Verlet), but I may be wrong.

Any insight is much appreciated.


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