Dear Gromacs users,<br>
<br>
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...<br>
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.<br>
Well any idea or comment about is welcome,<br>
<br>
Thank you very much in advance, <br>
Best regards<br>
<br>
Fernando Mattio<br>