Write parameters#
Writing the topology file for GROMACS.
The objective of this tutorial is to write the force field parameters (.itp files) for a simple system. If follows directly the writing of the gro file in Create conf.gro tutorial.
The parameter files created here will be used in Bulk salt solution. If you are only interested in running GROMACS, jump directly to Bulk salt solution.
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Default parameters#
Create a folder called ff/. Within ff/, create a new empty file named forcefield.itp, and copy the following in it:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 0.833
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
Na 11 22.9900 1.0000 A 0.23100 0.45000
OS 8 15.9994 -1.0000 A 0.38600 0.12
SO 16 32.0600 2.0000 A 0.35500 1.0465
HW 1 1.0079 0.5270 A 0.00000 0.00000
OW 8 15.9994 0.0000 A 0.31650 0.77323
MW 0 0.0000 -1.0540 D 0.00000 0.00000
[ bondtypes ]
; i j func b0 kb
SO OS 1 0.15 3.7656e4
[ angletypes ]
; i j k func theta k0
OS SO OS 1 109.5 520
The forcefield.itp file is used to define basic combination rules, as well as atom types, bond types, and angle types.
With comb-rule = 2, the mixing rule is calculated as \(\epsilon_{ij} = \sqrt{\epsilon_{ii} \epsilon_{jj}}\), \(\sigma_{ij} = (\sigma_{ii}+\sigma_{jj})/2\). FudgeLJ and fudgeQQ are the factors by which to multiply Lennard-Jones and Coulomb 1-4 interactions, respectively. You can refer to the GROMACS manual for more information.
The forcefield.itp file also contains information about the atoms, such their masses and Lennard-Jones parameters sigma and epsilon, as well as some parameters for the bond and angle constraints that will be necessary for the SO4 ions.
Notice that the particle with name MW is of type ‘D’ when all the other particles are of type ‘A’ for atoms. This is because MW is the virtual massless site of our 4 points rigid water model, see this wiki page for details.
Sodium ion#
Let us create a file named na.itp for the Sodium ion:
[ moleculetype ]
; molname nrexcl
Na 1
[ atoms ]
; id at-type res-nr res-name at-name cg-nr charge mass
1 Na 1 Na Na1 1 1.000 22.9900
The ‘molecule’ named Na for a residue with one single atom, of type Na and name Na1, charge +1.0 and mass 22.990 g/mol.
Sulfate ion#
The file so4.itp for the sulfate ion is more complicated, as the residue is made of 5 atoms that are bonded together and maintained by angular constrained.
The exclusions ensures that atoms from the same residue do not interact through LJ and Coulomb interactions.
[moleculetype]
; name nrexcl
SO4 1
[ atoms ]
; id at-type res-nr res-name at-name cg-nr charge mass
1 OS 1 SO4 O1 1 -1.000 15.9994
2 OS 1 SO4 O2 1 -1.000 15.9994
3 OS 1 SO4 O3 1 -1.000 15.9994
4 OS 1 SO4 O4 1 -1.000 15.9994
5 SO 1 SO4 S1 1 2.000 32.0600
[ bonds ]
; ai aj funct c0 c1
1 5 1 0.1520 3.7656e4
2 5 1 0.1520 3.7656e4
3 5 1 0.1520 3.7656e4
4 5 1 0.1520 3.7656e4
[ angles ]
; ai aj ak funct angle fc
1 5 2 1 109.5 520
1 5 3 1 109.5 520
1 5 4 1 109.5 520
2 5 3 1 109.5 520
2 5 4 1 109.5 520
3 5 4 1 109.5 520
[exclusions]
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
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Water molecule#
Finally, create a file named h2o.itp for the water molecule. Settle parameters are added to ensure that the residue remains rigid:
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at-type res-nr res-name at-name cg-nr charge mass
1 OW 1 SOL OW1 1 0.000 15.9994
2 HW 1 SOL HW1 1 0.527 1.0079
3 HW 1 SOL HW2 1 0.527 1.0079
4 MW 1 SOL MW1 1 -1.054 0.0000
[ settles ]
; i funct doh dhh
1 1 0.09572 0.15139
[ virtual_sites3 ]
; Vsite from funct a b
4 1 2 3 1 0.089608 0.089608
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
To continue and use those files for running a molecular dynamics simulation with GROMACS, go to Bulk salt solution.
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