fix amoeba/bitorsion command — LAMMPS documentation

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# fix amoeba/bitorsion command

## Syntax

    fix ID group-ID ameoba/bitorsion filename

- ID, group-ID are documented in fix command

- amoeba/bitorsion = style name of this fix command

- filename = force-field file with AMOEBA bitorsion coefficients

## Examples

    fix            bit all amoeba/bitorsion bitorsion.ubiquitin.data
    read_data      proteinX.data fix bit bitorsions BiTorsions
    fix_modify     bit energy yes

## Description

This command enables 5-body torsion/torsion interactions to be added to simulations which use the AMOEBA and HIPPO force fields. It matches how the Tinker MD code computes its torsion/torsion interactions for the AMOEBA and HIPPO force fields. See the Howto amoeba doc page for more information about the implementation of AMOEBA and HIPPO in LAMMPS.

Bitorsion interactions add additional potential energy contributions to pairs of overlapping phi-psi dihedrals of amino-acids, which are important to properly represent their conformational behavior. Each bitorsion interaction is thus defined for a 5-tuple of atoms \(IJKLM\) with bonds between successive atoms in the list, i.e. two overlapping dihedral interactions for atoms \(IJKL\) and \(JKLM\).

The examples/amoeba directory has a sample input script and data file for ubiquitin, which illustrates use of the fix amoeba/bitorsion command.

As in the example above, this fix should be used before reading a data file that contains a listing of bitorsion interactions. The filename specified should contain the bitorsion parameters for the AMOEBA or HIPPO force field.

The data file read by the read_data command must contain the topology of all the bitorsion interactions, similar to the topology data for bonds, angles, dihedrals, etc. Specifically it should have a line like this in its header section:

    N bitorsions

where \(N\) is the number of bitorsion 5-body interactions. It should also have a section in the body of the data file like this with \(N\) lines:

    BiTorsions

           1       1       8      10      12      18      20
           2       5      18      20      22      25      27
           [...]
           N       3     314     315     317      318    330

The first column is an index from 1 to \(N\) to enumerate the bitorsion 5-atom tuples; it is ignored by LAMMPS. The second column is the type of the interaction; it is an index into the bitorsion force field file. The remaining 5 columns are the atom IDs of the atoms (in order) for the 5-tuple \(IJKLM\), as described above.

Note that the bitorsions and BiTorsions keywords for the header and body sections match those specified in the read_data command following the data file name.

The data file should be generated by using the tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS data file from Tinker input files, including its PRM file which contains the parameters necessary for computing bitorsion interactions. The script must be invoked with the optional “-bitorsion” flag to do this; see the example for the ubiquitin system in the tools/tinker/README file. The same conversion script also creates the file of bitorsion coefficient data which is read by this command.

The potential energy associated with bitorsion interactions can be output as described below. It can also be included in the total potential energy of the system, as output by the thermo_style command, if the fix_modify energy command is used, as in the example above. See the note below about how to include the bitorsion energy when performing an energy minimization.

## Restart, fix_modify, output, run start/stop, minimize info

This fix writes the list of bitorsion interactions to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

The fix_modify energy option is supported by this fix to add the potential energy of the bitorsion interactions to both the global potential energy and peratom potential energies of the system as part of thermodynamic output or output by the compute pe/atom command. The default setting for this fix is fix_modify energy yes.

The fix_modify virial option is supported by this fix to add the contribution due to the bitorsion interactions to both the global pressure and per-atom stress of the system via the compute pressure and compute stress/atom commands. The former can be accessed by thermodynamic output. The default setting for this fix is fix_modify virial yes.

This fix computes a global scalar which can be accessed by various output commands. The scalar is the potential energy discussed above. The scalar value calculated by this fix is “extensive”.

No parameter of this fix can be used with the start/stop keywords of the run command.

The forces due to this fix are imposed during an energy minimization, invoked by the minimize command.

The fix_modify respa option is supported by this fix. This allows to set at which level of the r-RESPA integrator the fix is adding its forces. Default is the outermost level.

Note

For energy minimization, if you want the potential energy associated with the bitorsion terms forces to be included in the total potential energy of the system (the quantity being minimized), you MUST not disable the fix_modify energy option for this fix.

## Restrictions

To function as expected this fix command must be issued before a read_data command but after a read_restart command.

This fix can only be used if LAMMPS was built with the AMOEBA package. See the Build package page for more info.

## Related commands

fix_modify, read_data

## Default

none