[gmx-users] Adapting metallic ions from AMBER to GROMACS

Justin Lemkul jalemkul at vt.edu
Fri Apr 22 04:35:53 CEST 2016

On 4/21/16 4:30 PM, Pedro Lacerda wrote:
> Hi Mark,
> 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

It's force field convention, just different notation.  Sometimes different force 
fields or programs use Rmin/2, Rmin, or sigma.  They're easily converted, e.g.:

sigma = (Rmin/2)*2*2^(-1/6)

and in GROMACS the units are nm so you need an additional multiplication by 0.1 
to convert A -> nm.

> 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
> AMBER converted
> 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
> amber99sb-ildn.ff/ffnonbonded.itp
> 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
> relatively significant.

See above for the proper way to convert Rmin/2 to sigma.

As for Ca, probably the parameters are coming from a different source.  I don't 
know what "Table 2a" means or what paper it's from, but you need to verify that 
the source of parameters is compatible or that you understand where differences 
are coming from.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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