[CP2K-user] [CP2K:19536] Protein in solution - Dipole Moment

[Jürg Hutter]

Hi

because of a lack of detailed information I will guess what could be the problem.
I assume you are doing a QM calculation of the combined protein/water system.
The polarisation change (dipole) calculated with PBC (Berry phase algorithm) gives
results that depend on the branch of the complex logarithm. This can lead to
jumps by 2Pi/L (simple cubic case), see other discussions and literature about this.
Selecting a good reference point can avoid (or minimise) the number of jumps.
In any case, differences in polarisation (adjusted for jumps) will be independent
of the reference point.
A non-periodic calculation will not work if your system is truly periodic (protein + water).

regards
JH

________________________________________
From: 'up201... at g.uporto.pt' via cp2k <cp2k at googlegroups.com>
Sent: Sunday, November 19, 2023 3:48 PM
To: cp2k
Subject: [CP2K:19529] Protein in solution -  Dipole Moment

Dear CP2K community,

I am interested in measuring the dipole moment of a system which consists of a protein solvated in water and equilibrated in the NVT ensemble. The system is periodic in all directions to simulate the bulk solvent, under the assumption that the periodic image of the protein is far enough to avoid an electrostatic influence (common practice when simulating proteins). After doing some measurements of the dipole moment for a reactant and a transititon state structure of a reaction occuring at the active site, using as a REFERENCE_POINT the coordinates of an atom involved in the reaction and PERIODIC T, I noticed that the direction of dipole moment vector changes quite drastically (opposite direction), which is unexpected since the charge distribution remains virtually the same. Since the system is not truly periodic (proteins in aqueous solution are not periodic materials), I used PERIODIC F and now the dipole moment vectors are consistent. Thus, my question is: would it be correct to measure the dipole moment in this case with PERIODIC F, despite the cell definition being PERIODIC XYZ, or would it give an unphysical result?

Best regards,
Alex

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