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 (
. 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
On Thu, Mar 1, 2018 at 7:00 PM, Dan Gil <dan.gil9...@gmail.com> wrote:
> 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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