fix smd command — LAMMPS documentation

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# fix smd command

## Syntax

    fix ID group-ID smd type values keyword values

- ID, group-ID are documented in fix command

- smd = style name of this fix command

- mode = cvel or cfor to select constant velocity or constant force SMD

      cvel values = K vel
        K = spring constant (force/distance units)
        vel = velocity of pulling (distance/time units)
      cfor values = force
        force = pulling force (force units)

- keyword = tether or couple

      tether values = x y z R0
        x,y,z = point to which spring is tethered
        R0 = distance of end of spring from tether point (distance units)
      couple values = group-ID2 x y z R0
        group-ID2 = 2nd group to couple to fix group with a spring
        x,y,z = direction of spring, automatically computed with 'auto'
        R0 = distance of end of spring (distance units)

## Examples

    fix  pull    cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
    fix  pull    cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
    fix  stretch cterm smd cvel 20.0  0.0001 couple nterm auto auto auto 0.0
    fix  pull    cterm smd cfor  5.0 tether 25.0 25.0 25.0 0.0

## Description

This fix implements several options of steered MD (SMD) as reviewed in (Izrailev), which allows to induce conformational changes in systems and to compute the potential of mean force (PMF) along the assumed reaction coordinate (Park) based on Jarzynski’s equality (Jarzynski). This fix borrows a lot from fix spring and fix setforce.

You can apply a moving spring force to a group of atoms (tether style) or between two groups of atoms (couple style). The spring can then be used in either constant velocity (cvel) mode or in constant force (cfor) mode to induce transitions in your systems. When running in tether style, you may need some way to fix some other part of the system (e.g. via fix spring/self)

The tether style attaches a spring between a point at a distance of R0 away from a fixed point x,y,z and the center of mass of the fix group of atoms. A restoring force of magnitude K (R - R0) Mi / M is applied to each atom in the group where K is the spring constant, Mi is the mass of the atom, and M is the total mass of all atoms in the group. Note that K thus represents the total force on the group of atoms, not a per-atom force.

In cvel mode the distance R is incremented or decremented monotonously according to the pulling (or pushing) velocity. In cfor mode a constant force is added and the actual distance in direction of the spring is recorded.

The couple style links two groups of atoms together. The first group is the fix group; the second is specified by group-ID2. The groups are coupled together by a spring that is at equilibrium when the two groups are displaced by a vector in direction x,y,z with respect to each other and at a distance R0 from that displacement. Note that x,y,z only provides a direction and will be internally normalized. But since it represents the absolute displacement of group-ID2 relative to the fix group, (1,1,0) is a different spring than (-1,-1,0). For each vector component, the displacement can be described with the auto parameter. In this case the direction is re-computed in every step, which can be useful for steering a local process where the whole object undergoes some other change. When the relative positions and distance between the two groups are not in equilibrium, the same spring force described above is applied to atoms in each of the two groups.

For both the tether and couple styles, any of the x,y,z values can be specified as NULL which means do not include that dimension in the distance calculation or force application.

For constant velocity pulling (cvel mode), the running integral over the pulling force in direction of the spring is recorded and can then later be used to compute the potential of mean force (PMF) by averaging over multiple independent trajectories along the same pulling path.

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

The fix stores the direction of the spring, current pulling target distance and the running PMF 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 virial option is supported by this fix to add the contribution due to the added forces on atoms 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 no.

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.

This fix computes a vector list of 7 quantities, which can be accessed by various output commands. The quantities in the vector are in this order: the x-, y-, and z-component of the pulling force, the total force in direction of the pull, the equilibrium distance of the spring, the distance between the two reference points, and finally the accumulated PMF (the sum of pulling forces times displacement).

The force is the total force on the group of atoms by the spring. In the case of the couple style, it is the force on the fix group (group-ID) or the negative of the force on the second group (group-ID2). The vector values calculated by this fix are “extensive”.

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

## Restrictions

This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

## Related commands

fix drag, fix spring, fix spring/self, fix spring/rg, fix colvars, fix plumed

## Default

none

(Izrailev) Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, Wriggers, Schulten. Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.

(Park) Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

(Jarzynski) Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)