Lone pair forces

From: Hsubo Luo (luohsubo_at_gmail.com)
Date: Wed Dec 15 2021 - 11:15:40 CST

Hello NAMD developers and users,

I am new to NAMD but have some experience with other code (gromacs and lammps). My project is to use CHARMM force field with lone pair enabled on the halogen atom. My question is about how the force on the lone pair is distributed to the parent atoms. In my case, the force field topology has:

LONEPAIR COLI LP1 BRH CZ1 DIST 1.8900 SCAL 0.0

In psf file, I have the lines:

        96 288 !NUMLP NUMLPH
       2 1 F 1.8900 0.0000 0.0000
       2 4 F 1.8900 0.0000 0.0000
etc.

So it is the collinear lone pair.

Actually, I obtained some different results on gromacs with the virtual sites (https://urldefense.com/v3/__https://manual.gromacs.org/documentation/current/reference-manual/functions/interaction-methods.html*virtual-interaction-sites__;Iw!!DZ3fjg!u_r9z3z0MKumqyfF9ZCGSoUocT3EFOFKdyjM23CZNxDZ20QaljsjYvxUfx1-kdP_jQ$ <https://urldefense.com/v3/__https://manual.gromacs.org/documentation/current/reference-manual/functions/interaction-methods.html*virtual-interaction-sites__;Iw!!DZ3fjg!u_r9z3z0MKumqyfF9ZCGSoUocT3EFOFKdyjM23CZNxDZ20QaljsjYvxUfx1-kdP_jQ$ >). So I am suspecting that the treatment of force on lone pair can be the difference. Can you please tell how NAMD deals with this? I have searched on the web but no conclusion to date. Thank you in advance.

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