Force-fields#

GROMACS-SWAXS needs some extra files and information to be included in the force-field definitions, namely the Cromer-Mann parameters and neutron scattering lengths (NSLs) of all chemical elements and ions. To use a force field for SAS calculations, do the following:

Top force field file forcefield.itp#

Add

#ifdef SCATTER
  #include "cromer-mann-defs.itp"
  #include "neutron-scatt-len-defs.itp"
#endif

into the $GMXDATA/top/<forcefield>/forcefield.itp. This way, gmx grompp will read the Cromer-Mann and NSL definitions in $GMXDATA/top/cromer-mann-defs.itp and $GMXDATA/top/neutron-scatt-len-defs.itp.

Example: amber99sb-ildn.ff/forcefield.itp

Water and ion itp files#

In addition, the Cromer-Mann parameters and NSLs of water and ion atoms must be specified, for instance in <forcefield>/tip3p.itp and <forcefield>/ions.itp. Add a [ scattering_params ] block to the moleculetype definition of the water itp file:

#ifdef SCATTER
[ scattering_params ]
; i  ft    a1-a4, b1-b4, c
 1    1    CROMER_MANN_Owat
 2    1    CROMER_MANN_Hwat
 3    1    CROMER_MANN_Hwat

; i    ft    NSL
 1    2    NEUTRON_SCATT_LEN_O
 2    2    NSL_H_DEUTERATABLE
 3    2    NSL_H_DEUTERATABLE
#endif

Keys such as CROMER_MANN_Owat are defined in $GMXDATA/top/cromer-mann-defs.itp, while NEUTRON_SCATT_LEN_O are defined in $GMXDATA/top/neutron-scatt-len-defs.itp. The specific key NSL_H_DEUTERATABLE indicates that the deuteration of the water hydrogen atom is controlled with the mdp option waxs-deuter-conc.

Example: amber99sb-ildn.ff/tip3p.itp

Likewise add a [ scattering_params ] block into the moleculetype of all ions you plan to simulate. For chloride in an Amber force field, this would look like this:

[ moleculetype ]
; molname       nrexcl
CL              1

[ atoms ]
; id    at type         res nr  residu name     at name  cg nr  charge
1       Cl              1       CL              CL       1      -1.00000

#ifdef SCATTER
[ scattering_params ]
; i     ft      a1-a4, b1-b4, c
1       1       CROMER_MANN_Cl_minus
1       2       NEUTRON_SCATT_LEN_Cl
#endif

Example: amber99sb-ildn.ff/ions.itp

All modifications in the Charmm27 force field definitions are shown here: modifications of charmm27

Available force-fields#

We added Cromer-Mann and neutron scattering length definitions to most of the force fields provided with GROMACS by default, such as amber03.ff, amber99sb.ff, amber99sb-ildn.ff, charm27.ff, gromos54a7.ff, or oplsaa.ff.

In addition, for the convenience of the user, we added few more recent force fields taken from the GROMACS user contributions and from the Robert Best lab:

  • amber03ws

  • amber99sb-star-ildn

  • charmm22star

  • charmm36 from July 2021

Finally some extra water models were added:

  • charmm22star: tip4p2005, tip5ew

  • charmm27: tip4pew, tip4p2005, tip5pew

  • gromos54a7: tip4pew

  • oplsaa: tip4pew

You can make other force-fields work with GROMACS-SWAXS, with the modifications described above.

Note: the Cromer-Mann and NSL definitions of other moleculetypes than water or ions, in particular moleculetypes of proteins generated with gmx pdb2gmx, are created with gmx genscatt, see Usage.