PLUMED2 integration and metadynamics

[Input: recipes/moleculardynamics/plumed2/]

Metadynamics is a class of methods that are used to estimate free energy (and other state functions) of a system in cases where normal ergodic sampling is difficult due to the system’s energy landscape.

PLUMED2 is a molecular dynamics biasing and analysis package that has been interfaced with DFTB+ to give metadynamics and free energy sampling functionality. It can select a wide range of collective variables to sample systems, such as the distance between pairs of atoms or specified torsion angles.

To use PLUMED2, DFTB+ must be compiled with support for this enabled (and a compiled version of the plumed library available, see the plumed website). Set the Plumed tag in the Driver input block to Yes with VerlocityVerlet selected as the geometry driver. A plumed.dat input file must also be present in the run directory

Driver = VelocityVerlet{
 TimeStep [fs] = 1.0

 Plumed = Yes

 Thermostat = NoseHoover {
   Temperature [Kelvin] = 400
    CouplingStrength [cm^-1] = 3050
 }
.
.
.
}

The plumed.dat file contains information to be read by the PLUMED2 code that will allow it to either bias or analyse the molecular dynamics on the fly.:

DISTANCE ATOMS=4,9 LABEL=d1
DISTANCE ATOMS=5,9 LABEL=d2

METAD ...
LABEL=met ARG=d1,d2 PACE=100 HEIGHT=3 SIGMA=0.01,0.01
FILE=HILLS
BIASFACTOR=4 TEMP=400
... METAD

PRINT ARG=d1,d2 STRIDE=100 FILE=plumed_o.dat

ENDPLUMED

The first 2 lines of the example plumed.dat file tell PLUMED2 to define the distance between atoms 4 and 9 and the distance between atoms 5 and 9 and label them d1 and d2 respectively. the METAD tag tells plumed to read in parameters for a metadynamics bias calculation with d1 and d2 as input collective variables. This metadynamics simulation places a Gaussian hills function every 100 md steps. HEIGHT, SIGMA and BIASFACTOR are all metadynamics parameters while TEMP should correlate with the thermostat temperature. The Gaussian bias functions are written to the file specified by the FILE tag. The PRINT function tells PLUMED2 to print d1 and d2 every 100 steps to the file specified by the FILE tag. Finally, the ENDPLUMED tag indicates to PLUMED2 that input is complete.

More complete information on the functionality of PLUMED2 can be found in it’s user manual.