[gmx-users] Parmbsc1 force-field

[Viveca Lindahl]

Hi Dan,

No, it can be confusing. After reading your email I even dug up an old
email thread where we (confusedly) discussed this topic.

Most importantly is to not use the Na-parameters that I think are by
default present in the gromacs implementation, which leads to ion crystals
(DOI: 10.1021/jp0765392). The two references you cite, Smith & Dang 1994
and Dang 1995, are quite similar. I emailed with parmbsc1 developers and
their experience was the same. Together with parmbsc0, other authors have
used Dang 1995, so that's how our choice came about. To follow the parmbsc1
authors you should indeed use the paper they cite.



--
Viveca


On Mon, Mar 5, 2018 at 4:49 PM, Dan Gil <dan.gil9973 at gmail.com> wrote:

> 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?
>
> Best Regards,
>
> Dan
>
> On Mon, Mar 5, 2018 at 8:32 AM, Viveca Lindahl <vivecalindahl at gmail.com>
> wrote:
>
> > 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 :)
> >
> > --
> > Viveca
> >
> >
> > 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
> > 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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