[gmx-users] Parmbsc1 force-field

[Dan Gil]

Hi Dr. Lindahl,

Thank you for clarifying - it helps a lot!

Best Regards,

Dan

On Tue, Mar 6, 2018 at 6:20 AM, Viveca Lindahl <vivecalindahl at gmail.com>
wrote:

> 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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