"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

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fix restrain command :h3

[Syntax:]

fix ID group-ID restrain keyword args ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l
restrain = style name of this fix command :l
one or more keyword/arg pairs may be appended :l
keyword = {bond} or {angle} or {dihedral} :l
  {bond} args = atom1 atom2 Kstart Kstop r0
    atom1,atom2 = IDs of 2 atoms in bond
    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
    r0 = equilibrium bond distance (distance units)
  {angle} args = atom1 atom2 atom3 Kstart Kstop theta0
    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
    theta0 = equilibrium angle theta (degrees)
  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
    phi0 = equilibrium dihedral angle phi (degrees) :pre
:ule

[Examples:]

fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre

[Description:]

Restrain the motion of the specified sets of atoms by making them part
of a bond or angle or dihedral interaction whose strength can vary
over time during a simulation.  This is functionally similar to
creating a bond or angle or dihedral for the same atoms in a data
file, as specified by the "read_data"_read_data.html command, albeit
with a time-varying pre-factor coefficient, and except for exclusion
rules, as explained below.

For the purpose of forcefield parameter-fitting or mapping a molecular
potential energy surface, this fix reduces the hassle and risk
associated with modifying data files.  In other words, use this fix to
temporarily force a molecule to adopt a particular conformation.  To
create a permanent bond or angle or dihedral, you should modify the
data file.

NOTE: Adding a bond/angle/dihedral with this command does not apply
the exclusion rules and weighting factors specified by the
"special_bonds"_special_bonds.html command to atoms in the restraint
that are now bonded (1-2,1-3,1-4 neighbors) as a result.  If they are
close enough to interact in a "pair_style"_pair_style.html sense
(non-bonded interaction), then the bond/angle/dihedral restraint
interaction will simply be superposed on top of that interaction.

The group-ID specified by this fix is ignored.

The second example above applies a restraint to hold the dihedral
angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
restraint coefficient.  The fourth example applies similar restraints
to multiple dihedral angles using a restraint coefficient that
increases from 0.0 to 2000.0 over the course of the run.

NOTE: Adding a force to atoms implies a change in their potential
energy as they move due to the applied force field.  For dynamics via
the "run"_run.html command, this energy can be added to the system's
potential energy for thermodynamic output (see below).  For energy
minimization via the "minimize"_minimize.html command, this energy
must be added to the system's potential energy to formulate a
self-consistent minimization problem (see below).

In order for a restraint to be effective, the restraint force must
typically be significantly larger than the forces associated with
conventional forcefield terms.  If the restraint is applied during a
dynamics run (as opposed to during an energy minimization), a large
restraint coefficient can significantly reduce the stable timestep
size, especially if the atoms are initially far from the preferred
conformation.  You may need to experiment to determine what value of K
works best for a given application.

For the case of finding a minimum energy structure for a single
molecule with particular restratins (e.g. for fitting forcefield
parameters or constructing a potential energy surface), commands such
as the following may be useful:

# minimize molecule energy with restraints
velocity all create 600.0 8675309 mom yes rot yes dist gaussian
fix NVE all nve
fix TFIX all langevin 600.0 0.0 100 24601
fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $\{angle1\} dihedral 3 1 2 9 0.0 5000.0 $\{angle2\}
fix_modify REST energy yes
run 10000
fix TFIX all langevin 0.0 0.0 100 24601
fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $\{angle1\} dihedral 3 1 2 9 5000.0 5000.0 $\{angle2\}
fix_modify REST energy yes
run 10000
# sanity check for convergence
minimize 1e-6 1e-9 1000 100000
# report unrestrained energies
unfix REST
run 0 :pre

:line

The {bond} keyword applies a bond restraint to the specified atoms
using the same functional form used by the "bond_style
harmonic"_bond_harmonic.html command.  The potential associated with
the restraint is

:c,image(Eqs/bond_harmonic.jpg)

with the following coefficients:

K (energy/distance^2)
r0 (distance) :ul

K and r0 are specified with the fix.  Note that the usual 1/2 factor
is included in K.

:line

The {angle} keyword applies an angle restraint to the specified atoms
using the same functional form used by the "angle_style
harmonic"_angle_harmonic.html command.  The potential associated with
the restraint is

:c,image(Eqs/angle_harmonic.jpg)

with the following coefficients:

K (energy/radian^2)
theta0 (degrees) :ul

K and theta0 are specified with the fix.  Note that the usual 1/2
factor is included in K.

:line

The {dihedral} keyword applies a dihedral restraint to the specified
atoms using a simplified form of the function used by the
"dihedral_style charmm"_dihedral_charmm.html command.  The potential
associated with the restraint is

:c,image(Eqs/dihedral_charmm.jpg)

with the following coefficients:

K (energy)
n = 1
d (degrees) = phi0 + 180 :ul

K and phi0 are specified with the fix.  Note that the value of n is
hard-wired to 1.  Also note that the energy will be a minimum when the
current dihedral angle phi is equal to phi0.

:line

[Restart, fix_modify, output, run start/stop, minimize info:]

No information about this fix is written to "binary restart
files"_restart.html.

The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential energy associated with this fix to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.

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

NOTE: If you want the fictitious potential energy associated with the
added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.

This fix computes a global scalar, which can be accessed by various
"output commands"_Section_howto.html#howto_15.  The scalar is the
potential energy for all the restraints as 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"_run.html command.

[Restrictions:] none

[Related commands:] none

[Default:] none
