pesmd
 This is part of the cltools module

Pesmd allows one to do (biased) Langevin dynamics on a two-dimensional potential energy surface.

The energy landscape that you are moving about on is specified using a plumed input file. The directives that are available for this command line tool are as follows:

Compulsory keywords
 nstep The number of steps of dynamics you want to run temperature ( default=NVE ) the temperature at which you wish to run the simulation in LJ units friction ( default=off ) The friction (in LJ units) for the langevin thermostat that is used to keep the temperature constant tstep ( default=0.005 ) the integration timestep in LJ units dimension the dimension of your energy landscape plumed ( default=plumed.dat ) the name of the plumed input file containing the potential ipos ( default=0.0 ) the initial position of the system idum ( default=0 ) The random number seed
Options
 periodic ( default=on ) are your input coordinates periodic min minimum value the coordinates can take for a periodic domain max maximum value the coordinates can take for a periodic domain
Examples

You run a Langevin simulation using pesmd with the following command:

plumed pesmd < input


The following is an example of an input file for a pesmd simulation. This file instructs pesmd to do 50 steps of Langevin dynamics on a 2D potential energy surface at a temperature of 0.722

temperature 0.722
tstep 0.005
friction 1
dimension 2
nstep 50
ipos 0.0 0.0


If you run the following a description of all the directives that can be used in the input file will be output.

plumed pesmd --help


The energy landscape to explore is given within the plumed input file. For example the following example input uses MATHEVAL to define a two dimensional potential.

d1: DISTANCE ATOMS=1,2 COMPONENTS
ff: MATHEVAL ARG=d1.x,d1,y PERIODIC=NO FUNC=()
bb: BIASVALUE ARG=ff


Atom 1 is placed at the origin. The x and y components on our surface are the positions of the particle on our two dimensional energy landscape. By calculating the vector connecting atom 1 (the origin) to atom 2 (the position of our particle) we are thus getting the position of the atom on the energy landscape. This is then inserted into the function that is calculated on the second line. The value of this function is then used as a bias.

We can also specify a potential on a grid and look at the dynamics on this function using pesmd. A plumed input for an example such as this one might look something like this:

d1: DISTANCE ATOMS=1,2 COMPONENTS
bb: EXTERNAL ARG=d1.x,d1,y FILE=fes.dat


In this way we can use pesmd to do a dynamics on a free energy surface calculated using metadynamics and sum_hills. On a final note once we have defined our potential we can use all the biasing functions within plumed in addition in order to do a biased dynamics on the potential energy landscape of interest.