Steered Molecular Dynamics - Trebonius91/utils4VASP GitHub Wiki
Biased molecular dynamics, with rigid or moving bias potentials on certain variables of the system, can be useful for many tasks, e.g., investigating reaction mechanisms or transport processes in real time.
A particular part is steered MD, in which a time-dependent umbrella potential is applied to the coordinates of interest, which, e.g., drive the system from reactants to products state within some ps of dynamics.
Take the INCAR file (and other input files) of a typical AIMD simulation (see here) and add the following keywords to it:
SPRING_K [value1] [value2] ...Strength of the force constant(s) of the harmonic umbrella potential(s), in eV/A. The exact values depend on the system and the desired length of the steered MD trajectory. For short trajectories and high potential energy barriers along reaction paths, higher values might be used. If the values are too large, however, the molecule might be torn apart. Good values seem to be between 2.0 and 6.0. For each coordinate to be biased, one extra value need to be added after the keyword!SPRING_R0 [value1] [value2] ...The initial position(s) of the umbrella potential(s) with respect to the chosen coordinate (e.g., the initial length of the bond to be elongated). One value per biased coordinate need to be added, ideally matching the current values in thePOSCARfile.SPRING_V0 [value1] [value2] ...The movement speed(s) of the umbrella potential position(s) during the trajectory, in Angstrom/fs (distances) or rad/fs (angles). The value should be precalculated, such that within the given number of simulation steps (NSW), the desired final values of the coordinate(s) are reached. Positive values will enlarge the initial value of the coordinate, negative values will shrink it. Again, one value per biased coordinate must be given.
Additionally, a separate input file named ICONST containing the restrains and constraints withhin the system must be given (else, all SPRING keywords in the INCAR will be ignored without further notice!). In this file, all coordinates on which umbrella potentials shall be applied must be given. If, e.g., an umbrella potential shall be applied on the distance between the atoms 3 and 4, the following line is sufficient:
R 3 4 8
The last number (8) is called the "Status flag" and specifies the application of a harmonic potential. For two separate coordinates steered during the same trajectory, two lines are needed (and two values for each SPRING keyword!):
R 11 12 8
R 13 14 8
Alternatively, one can define composite coordinates like the distance between the center of masses of two bonds in the system. If one bond exists between atoms 11 and 13 and another between atoms 12 and 14, the composite coordinate would be the following:
B 11 13 12 14 8
More details on several more complicated coordinates to be defined in the ICONST file can be found in the VASP Wiki.
During a steered MD simulation or after it, the current status can be evaluated by invoking the [eval_steered](add link) program in the main folder of the calculation.