Dear all,

I'm attempting to run NPT on water molecules. When constructing the system with the aid of amorphous module I can notice a cubic box is created (see images 1, 2 attached). image 3 shows this cubic box after geometry optimization. Next I do NVT (please notice images 4 to 7). After this when doing NPT the simulation cell takes a triclinic shape whereas I was expecting to get a cubic box (see image 8). 

I suppose the issue arises when generating the box during construction stage using amorphous tool (please see image 1). Nevertheless, I'm a bit confounded how come image 2 is showing a cubic box has been created. 

Could you please take a look at the images attached and provide some insights into whats going on with this.

Much appreciated,

Serene

--- Dynamics parameters ----

Ensemble : NPT
Temperature : 353.00 K
Control method : Berendsen
Decay constant : 0.1000000 ps
Pressure : 0.0001 GPa
Control method : Parrinello
Cell time constant : 1.0000000 ps
Timestep : 0.50 fs
Number of steps : 2000000
Duration : 1000 ps
Initial velocities : Current
Random number seed : 1644281483

---- Energy parameters ----

Forcefield : COMPASSIII (Version 1.1)
Charges : Forcefield assigned
Electrostatic terms:
Summation method : Ewald
Accuracy : 0.0001 kcal/mol
Buffer width : 0.5 A

van der Waals terms:
Summation method : Atom based
Truncation method : Cubic spline
Cutoff distance : 15.5 A
Spline width : 1 A
Long range correction : YES
Buffer width : 0.5 A