[CP2K-user] [CP2K:21299] NPT box size not reaching equilibrium with multiple atomic constraints

[Krack Matthias]

Hi Sean

Are you sure that the FF is set up properly, in particular, did you check if the values for EI_SCALE14<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD.html#CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.EI_SCALE14> and VDW_SCALE14<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD.html#CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.VDW_SCALE14> are correct?

Best

Matthias

From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Sean Larmore <sean.larmore at gmail.com>
Date: Tuesday, 18 March 2025 at 21:48
To: cp2k <cp2k at googlegroups.com>
Subject: [CP2K:21297] NPT box size not reaching equilibrium with multiple atomic constraints
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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