First of all, I would like to say that this is a great work being accomplished by this group.

Secondly, I have a doubt about the parametrization of the PF6- anion, I know that the .ff files have the citations of the articles from which the bonds and angles parameters are taken, however I noticed that in the AMBER parametrization of this anion it is usual to consider two terms in the angles harmonic potentials, both with the same force constants but with different equilibrium angles: 90 and 180 degrees.

The force field provided in the files has just one term with the equilibrium angle of 90 degrees. I would like to know if just this single term in the angles part of the potential exists or if it is necessary to add the other term with the other equilibrium angle. In fact, I’m doing some molecular dynamics in LAMMPS and the potential energy is indeed to high with the angles potential contributing with most of it.

Hello,
In PF6- there is ambiguity because F-P-F angles can have two values: 90 and 180. Thus there are three 180 degree angles that should not be included. Recent versions of the force field tool (https://github.com/agiliopadua/fftool) will not include the 180 angles automatically when generating input files for MD simulations.
Agilio

Dear prof. Padua, first of all I want to congrat for this work, which has been very helpful for me.

Secondly, I have a question about some parameters of the force field. Basically, I can’t find a corrispondence between some parameters as they are published in J. Phys. Chem. B 2004, 108, 2038-2047 (plus. supp. info) and those ones I’ve found in github.com. For example, in github I find:

[bonds]
Cr-Na 1.315 3992

but in the article the value of the constant for this bond is 1996 KJ/(mol A^2). This happens for various bonds and angles constants. Plus, some authors that have done force fields based on yours report the github values in their articles (es. Zhao 2007), but others use the article ones (es. Kodderman 2007). Is there something I’m missing?

Thank you for your answer, this would really help me.

Unfortunately some mistakes crept into the papers. Sorry for that.
One common is dividing harmonic force constants by 2 (some codes and force fields to it like that).

Normally the values in the files on GitHub are the good ones.
Don’t hesitate to ask in case of doubt.

First of all, I would like to say that this is a great work being accomplished by this group.

Secondly, I have a doubt about the parametrization of the PF6- anion, I know that the .ff files have the citations of the articles from which the bonds and angles parameters are taken, however I noticed that in the AMBER parametrization of this anion it is usual to consider two terms in the angles harmonic potentials, both with the same force constants but with different equilibrium angles: 90 and 180 degrees.

The force field provided in the files has just one term with the equilibrium angle of 90 degrees. I would like to know if just this single term in the angles part of the potential exists or if it is necessary to add the other term with the other equilibrium angle. In fact, I’m doing some molecular dynamics in LAMMPS and the potential energy is indeed to high with the angles potential contributing with most of it.

Hello,

In PF6- there is ambiguity because F-P-F angles can have two values: 90 and 180. Thus there are three 180 degree angles that should not be included. Recent versions of the force field tool (https://github.com/agiliopadua/fftool) will not include the 180 angles automatically when generating input files for MD simulations.

Agilio

Dear prof. Padua, first of all I want to congrat for this work, which has been very helpful for me.

Secondly, I have a question about some parameters of the force field. Basically, I can’t find a corrispondence between some parameters as they are published in J. Phys. Chem. B 2004, 108, 2038-2047 (plus. supp. info) and those ones I’ve found in github.com. For example, in github I find:

[bonds]

Cr-Na 1.315 3992

but in the article the value of the constant for this bond is 1996 KJ/(mol A^2). This happens for various bonds and angles constants. Plus, some authors that have done force fields based on yours report the github values in their articles (es. Zhao 2007), but others use the article ones (es. Kodderman 2007). Is there something I’m missing?

Thank you for your answer, this would really help me.

Kind regards,

Matteo Busato

Hi,

Unfortunately some mistakes crept into the papers. Sorry for that.

One common is dividing harmonic force constants by 2 (some codes and force fields to it like that).

Normally the values in the files on GitHub are the good ones.

Don’t hesitate to ask in case of doubt.

Regards,

Agilio