Solvent Box

From: Jon Kusner (
Date: Wed Jun 26 2013 - 12:15:31 CDT


We have been trying to create an acetonitrile solvent box. We have been
following the instructions of other troubleshooters and looking on other
forums for guidance but have still not been successful. Currently we have a
psf of our final solvent box, a 12x12x12 array of acetonitrile molecules,
that we are trying to equilibrate. Whenever we try to run
an equilibration we get through 3000 step of minimization but as soon as
the program begins molecular dynamics we receive the error:
Fatal error on PE 2> Fatal Error: Periodic cell has become too small for
original patch grid!
Possible solutions are to restart from a recent checkpoint, increase
margin, or disable useflexiblecell for liquid simulation.
We have tried each of these possible solutions and received the same
result. If there is any guidance we could receive it would be much
appreciated. Thank you for all of your help.


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