[gmx-users] Parmbsc1 force-field

[Mark Abraham]

Hi,

This is not an official GROMACS offering, so as always, buyer beware. But
the forcefield.doc file notes the source of the Na+ parameters as
https://pubs.acs.org/doi/abs/10.1021/ja00131a018. Does that cover the
question?

Mark

On Fri, Mar 2, 2018 at 5:20 PM Dan Gil <dan.gil9973 at gmail.com> wrote:

> Hello, update here.
>
> I think there is a possibility that the parmbsc1 force-field updated on the
> gromacs website has some incorrect values.
>
> In the parmbsc1 paper (https://www.nature.com/articles/nmeth.3658.pdf)
> they
> say they use Na+ parameters from this paper (
> http://aip.scitation.org/doi/pdf/10.1063/1.466363).
>
> .        sigma (Å)    epsilon (kcal/mol)
> Na+   2.350          0.1300
>
> Here is what I find in the GROMACS force-field.
>
> .        sigma (nm)    epsilon (kJ/mol)
> Na+   0.2584        0.4184
>
> I would like to directly contact the author, but I have no means at the
> moment.
>
> Best Regards,
>
> Dan
>
> On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9973 at gmail.com> wrote:
>
> > Hi,
> >
> > I am using the parmbsc1 force-field (http://www.gromacs.org/@api/d
> > eki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the
> > original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are coming
> > from, but I am having trouble finding them.
> >
> > The Amber17 manual suggests that this paper (
> https://pubs.acs.org/doi/pdf/
> > 10.1021/ct500918t) is the source for monovalent ions. But, the values
> > from the GROMACS parmbsc1 force-field (ffnonbonded.itp) does not match
> the
> > values from the paper, I think.
> >
> > Could you point me to the right direction? Citing the original paper is
> > something important to me, but I have apparently hit a dead end.
> >
> > Best Regards,
> >
> > Dan Gil
> > PhD Student
> > Department of Chemical and Biomolecular Engineering
> > Case Western Reserve University
> >
> --
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