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.