What are ion parameters used in Gromacs?

User discussions
1

Does anybody know what the default ion parameters are used in Gromacs?
E.g., In the directory for the parameters of Amber99sb-ildn, ion parameters are given,
but I’m unsure what they actually are.
Presumably, could it be Joung-Cheatham parameters?

Thanks in advance :)

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2

Hi,
If you select a “force field”, GROMACS will use the parameter located in the “force field” directories to perform the simulations.
If you select Amber99sb-ildn, the parameters defined in …/share/gromacs/top/amber99sb-ildn.ff/nonbonded.itp will be used for non-bonded interactions. The file …/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc provides the force field reference.
Unfortunately not always the source of the ions parameters is clearly stated in the ref publication. Sometimes comments in the ffnonbonded.itp files are added to specify the source of ion parameters. Here you may also find useful information, Force fields in GROMACS — GROMACS 2022.2 documentation
If none of the options works for your case, you can contact the force field authors or check your self from parameter values in ffnonbonded.itp.

I hope it helps.
\Alessandra

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3

Hi,

Thank you for your help.

I noticed that the file amber99sb-ildn.ff/amber99sb-ildn.ff includes the following lines:

Cl                35.45000      ; chlorine  (Applequist)
Na                22.99000      ; Na+, ions pol:J.PhysC,11,1541,(1978)

Does this imply that Chloride’s parameter is from Applequist and sodium’s from J.PhysC,11,1541,(1978)?

I think that the reference for Cl may be:
Applequist, J., Carl, J. R. & Fung, K.-K. Atom dipole interaction model for molecular polarizability. Application to polyatomic molecules and determination of atom polarizabilities. J. Am. Chem. Soc. 94, 2952–2960 (1972)

The ref for Na would be:
Sangster, M. J. L. & Atwood, R. M. Interionic potentials for alkali halides. II. Completely crystal independent specification of Born-Mayer potentials. J. Phys. C: Solid State Phys. 11, 1541 (1978)

However, I am still unsure if they are exactly the references for the ion parameters…
I tried to compare the values in the refs with ffnonbonded.itp, but the values for Na seem different and I couldn’t find the parameters for Cl in Applequist’s paper…

I am still not sure what ion parameters are stored in /share/top/ directories and to who I should contact.

Thanks,

4

Hi,
the best is ask to the AmberSB99-ildn force field developers/expert. The AMBER force fields in GROMACS are ported from the original AMBER force field files.
The tool used to create the AmberSB99 port is ffamber (AMBER force field ports for the GROMACS) Sorin Lab ffAMBER website (as reported in the forcefield.doc file) and AmberSB99 and AmberSB99-ildn have the same ffnonbonded.itp

Of course, it may be someone else in the forum knows more.

\Alessandra

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5

Thank you. I really appreciate it :)

6

Charge and mass are probably all the same, so it’s just LJ parameters that you want to check. I’m looking at gromacs 2022.2, and the file naming appears different than why you have, but I suspect the content is the same.

NA is atom type Na:

grep NA amber99sb-ildn.ff/ions.itp
NA 1
1 Na 1 NA NA 1 1.00000

CL is atom type Cl:

grep CL amber99sb-ildn.ff/ions.itp
CL 1
1 Cl 1 CL CL 1 -1.00000

Find their non bonded parameters in ffnonbonded.itp:

grep Na amber99sb-ildn.ff/ffnonbonded.itp
Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
grep Cl amber99sb-ildn.ff/ffnonbonded.itp
Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01

All amber ff variants use the same Na/Cl LJ parameters in gromacs:

grep Na amber*/ffnonbonded.itp |column -t
amber03.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
amber94.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
amber96.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
amber99.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
amber99sb.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
amber99sb-ildn.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
amberGS.ff/ffnonbonded.itp:Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
grep Cl amber*/ffnonbonded.itp |column -t
amber03.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
amber94.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
amber96.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
amber99.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
amber99sb.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
amber99sb-ildn.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
amberGS.ff/ffnonbonded.itp:Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01

Chen and Pappu list these same values for Amber99: https://pubs.acs.org/doi/10.1021/jp0765392
That paper (2007) and the Joung paper (2008) both came well after the amber99 force field was introduced.

I think the Na+ parameters are modifications from Aqvist’s JPC 1990 parameters to meet the amber functional form. If you really want to track these down, the amber mailing list would be a good place to start.

Note that the Applequist info is a false lead. What you show is just atomic mass, and Applequist was working with molecular chlorine, not chloride ion.

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7

Thanks for giving me helpful information and correcting me.
I’ve read the paper ( https://pubs.acs.org/doi/10.1021/jp0765392 ) you shared and confirmed that it shows the ion vdw parameters.

Based on your advice, I’ll look for where the original vdw parameters come from.

8

Hello, have you figured out what ion parameters are used in Gromacs? I’ve had the same question. I’m interested in using the NaCl parameters of Joung and Cheatham