[gmx-users] Parmbsc1 force-field

[Dan Gil]

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
>