[gmx-users] Parmbsc1 force-field
dan.gil9973 at gmail.com
Mon Mar 5 16:50:02 CET 2018
Hi Dr. Lindahl,
Thanks for putting the force-field together! It is helping my research very
much. Right now I am just checking over everything to make sure I didn't
make any silly mistakes, and that everything is justified.
I might be just confusing myself, but the parmbsc1 paper is citing this
paper (http://aip.scitation.org/doi/pdf/10.1063/1.466363) for the Na+
parameters... whereas the citation for the force-field you put together is
this one (https://pubs.acs.org/doi/abs/10.1021/ja00131a018). They have
different values for the 12-6 sigma and epsilon.
Same authors, but the one you chose is a newer work than the other one. Is
that why you chose the parameters from this paper?
On Mon, Mar 5, 2018 at 8:32 AM, Viveca Lindahl <vivecalindahl at gmail.com>
> Hi Dan,
> I'm the author together (with Alessandra Villa). I hope it helps others
> providing the parameters on the website, but as Mark said, it's up to you
> to double-check it. If you do find actual errors, I'm interested in hearing
> about it :)
> On Fri, Mar 2, 2018 at 5:19 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
> > 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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