[gmx-users] Adapting metallic ions from AMBER to GROMACS
pslacerda+gmx at gmail.com
Thu Apr 21 22:30:30 CEST 2016
I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.
Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results
AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01
I got exact matches for epsilon in Zn and Mg, but not for Ca. Also the
difference on sigma was in the order Å/10, except for Zn which was
(I'm expecting that Mailman render the table into plain text relatively
well, so if this post go with bad formatting I'll post again)
2016-04-18 21:29 GMT-03:00 Mark Abraham <mark.j.abraham at gmail.com>:
> Convert the units and absorb the factor of two to the minus six. Compare
> with other ions present in both representations of such force fields.
> On Tue, 19 Apr 2016 02:21 Pedro Lacerda <pslacerda+gmx at gmail.com> wrote:
> > Hi Gromacs users,
> > We are planning a simulation with a metallic (fe+2) attached on the
> > protein. The parameters found in  cannot be directly inserted on
> > ffnonbonded.itp because equation 1 of  and equation 4.5 of  are
> > slightly different.
> > Theoreticaly these Lennard-Jones parameters could be used in any PME
> > force field, but it was derived and tested using the AMBER software and
> > potential, so it is our current force field of choice. In
> > amber99sb-ildn/ffnonbonded.itp the long range interactions are described
> > terms of epsilon (kJ/mol) and sigma (Rmin; nm).
> > Eq 1:
> > Lj = 4e ((R/r)^12 - (R/r)^6)
> > Eq 4.5:
> > Lj = e ((R/r)^12 - 2(R/r)^6)
> > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> > calculations to optimize the software. But this occurs at implementation
> > level and probably does not have correspondence with the paper.
> > My question is how can I adapt these parameters so they can be used in
> > Gromacs?
> > (Sorry about the previous email, now the title is correct)
> > 
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
> >  ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
> >  http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
> > Cheers,
> > Pedro Lacerda
> > --
> > 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-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users