[CP2K-user] [CP2K:21297] NPT box size not reaching equilibrium with multiple atomic constraints

[Sean Larmore]

Hi CP2K community, 

I am trying to run an npt simulation on a molecule containing Boron with 
the generalized amber force field (GAFF). GAFF does not contain parameters 
for Boron, so I had set up these simulations to keep the Boron atom (and 
it's connected bonds, angles, and dihedrals) constrained/frozen. However, I 
quickly noticed that the box size would not equilibrate and hovered around 
the initial box size, leading to significant void spaces in my solvent, 
poor solvent density, and solvent distribution. 

I set up some control tests on a different molecule without Boron, so I 
knew the FF would not cause issues, and found that the issue seems to be 
caused by atomic constraints. As you can see in the attached graphs, with 
no constraints the edge length of the box reaches an equilibrium value of 
~23A, with one constraint it also goes to ~23A, with two constraints it 
goes to ~24.5A, and with three constraints it goes to ~26.5A (3.5A larger 
than the box without atomic constraints). This essentially makes it 
impossible to have more than 1 or 2 constraints on a system as it goes 
through an npt, as the box size will never reach the correct equilibrium 
size. This also precludes me from my goal of simulating the boron 
containing molecule I'm currently interested, as I need a minimum of 7 
constraints. 

Does anyone have any insight into this problem with npt simulations and 
constraints and/or a potential work around in CP2K? I've also attached my 
input and output files for one of the constrained jobs. 

Thanks in advance,
Sean

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