[gmx-users] Fatal error: The X-size of the box times triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

[Kevin C Chan]

Dear Users,

I have encountered "Fatal error: The X-size of the box times triclinic skew
factor is smaller than the number of DD cells times the smallest allowed
cell size" during a pre-equilibrium (NPT) run. It is NOT an annealing
process and temperature was coupled to 300K, pressure to 1.0 bar. It was a
1000-water plus 100 amino acid system.

I have gone through the mailing archive and it was reported that this might
result from too-fast-shrinking systems. However I intended to shrink the
box during the NPT run as initially it was generated using genbox tool and
what I wanted to fix is only the number of solvent and additional
particles. As I do not know the suitable box size for the system so I guess
a little bigger box size (6 nm) and let it shrink during the NPT run. This
was successful with a previous system (1000 water, 50 amino acids) and the
box size shrank to 4.X nm.

Would this be a wrong approach? And how could I deal with the reported
error?

Thanks in advance,

Kevin
City University of Hong Kong