[gmx-users] Box dimension size errors in MARTINI soft core simulation

[Scott Pendley]

I am fairly new to gromacs and I am trying to run a thermodynamic
integration simulation of a ligand disappearing in a box of octanol at a
single set lambda point.  I have previous successful nvt and npt runs of
this system.  When I have added the free energy portions to the input file,
I get the following error:

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

This seems unusual.  The box dimensions are 9.45 nm x 9.45 x 9.45 nm so
that is fairly large even accounting for some shrinkage with a disappearing
ligand.

Cutoffs in the input file are set as follows: rlist =1.4, rvdw=1.2,
rcoulomb=1.2.  Doubling any of them would still be less than 3 nm which is
significantly smaller than the box size.  Is there anything I am missing or
any suggestions that others can give me?

Thank you,

Scott