[gmx-users] water in cubic box exploding

Fernando Mattio mattiofer at gmail.com
Mon Jan 30 16:09:15 CET 2006

Dear Gromacs users,

I simulated for few picoseconds (50 ps) my system (protein next to ice
plane, in a cubic box solvated with water) in different box sizes. In the
simulations with cubic box from 8 nm until 11 nm something weird occurs, the
water seems not to respect the cubic box limits and expands, growing a lot
and getting other non sense formats...
However, when I tried with 12 nm, and for a longer time (200 ps) nothing
occurs, I mean the cubic boc is "respected" during all the simulation. The
parameter file and other files are very similar in all cases, then until the
moment I did not figure out why these two distincts behaviors occurs. I
tried to establish the pressure, in all cases, of 1 bar, and temperature of
263 K. In the box with 12 nm average values are 284 K and 4,5 bar, but for
example with the 9nm box the values are 276,33K and 253 bar! But all the
simulations runned until the end. Strange also  that in both cases the
values are not exactly the ones I chosed in the parameter file.
Well any idea or comment about is welcome,

Thank you very much in advance,
Best regards

Fernando Mattio
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