fix neb command — LAMMPS 15 May 2015 version documentation

# fix neb command

## Syntax

    fix ID group-ID neb Kspring

- ID, group-ID are documented in fix command
- neb = style name of this fix command
- Kspring = inter-replica spring constant (force/distance units)

## Examples

    fix 1 active neb 10.0

## Description

Add inter-replica forces to atoms in the group for a multi-replica simulation run via the neb command to perform a nudged elastic band (NEB) calculation for transition state finding. Hi-level explanations of NEB are given with the neb command and in Section_howto 5 of the manual. The fix neb command must be used with the “neb” command to define how inter-replica forces are computed.

Only the N atoms in the fix group experience inter-replica forces. Atoms in the two end-point replicas do not experience these forces, but those in intermediate replicas do. During the initial stage of NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting on the atoms of each intermediate replica I is altered, as described in the (Henkelman1) paper, to become:

    Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That

Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its neighbor replicas. That (t with a hat over it) is the unit “tangent” vector for replica I which is a function of Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points roughly in the direction of (Ri+i - Ri-1); see the (Henkelman1) paper for details.

The first two terms in the above equation are the component of the interatomic forces perpendicular to the tangent vector. The last term is a spring force between replica I and its neighbors, parallel to the tangent vector direction with the specified spring constant Kspring.

The effect of the first two terms is to push the atoms of each replica toward the minimum energy path (MEP) of conformational states that transition over the energy barrier. The MEP for an energy barrier is defined as a sequence of 3N-dimensional states which cross the barrier at its saddle point, each of which has a potential energy gradient parallel to the MEP itself.

The effect of the last term is to push each replica away from its two neighbors in a direction along the MEP, so that the final set of states are equidistant from each other.

During the second stage of NEB, the forces on the N atoms in the replica nearest the top of the energy barrier are altered so that it climbs to the top of the barrier and finds the saddle point. The forces on atoms in this replica are described in the (Henkelman2) paper, and become:

    Fi = -Grad(V) + 2 (Grad(V) dot That) That

The inter-replica forces for the other replicas are unchanged from the first equation.

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

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. 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, as invoked by the minimize command via the neb command.

## Restrictions

This command can only be used if LAMMPS was built with the REPLICA package. See the Making LAMMPS section for more info on packages.

## Related commands

neb

Default: none

(Henkelman1) Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).

(Henkelman2) Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000).