Yes! Thank you so much. On Fri, Mar 2, 2018 at 11:37 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> Hi, > > This is not an official GROMACS offering, so as always, buyer beware. But > the forcefield.doc file notes the source of the Na+ parameters as > https://pubs.acs.org/doi/abs/10.1021/ja00131a018. Does that cover the > question? > > Mark > > On Fri, Mar 2, 2018 at 5:20 PM Dan Gil <dan.gil9...@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.gil9...@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 > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.