Command line tool: pesmd

Module	cltools
Description	Input
Langevin dynamics on PLUMED energy landscape	file

Details

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 in a plumed input file. For example the following example input uses MATHEVAL to define a two dimensional potential.

Click on the labels of the actions for more information on what each action computes

d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
ffThe MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d1.x,d1.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x*x+y*y
bbThe BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Type   
 Description  
bb.bias
scalar
the instantaneous value of the bias potential
bb.ff_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named ff: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=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. To do so you would use the DISTANCE command as in the input above together with an EXTERNAL action that takes d1.x and d1.y as arguments. In this way you can use pesmd to do a dynamics on a free energy surface calculated using metadynamics and sum_hills. Notice also, that 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.

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

plumed pesmdLangevin dynamics on PLUMED energy landscape More details < input This is the input file for the calculation.
The pesmd action with label plumed calculates something

The input to pesmd is specified in an input file that contains one directive per line like the one shown below.

#TOOL=pesmdLangevin dynamics on PLUMED energy landscape This action has hidden defaults. More details
temperature the temperature at which you wish to run the simulation in LJ units 0.722
tstep the integration timestep in LJ units 0.005
friction The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant 1
dimensionthe dimension of your energy landscape 2
nstepThe number of steps of dynamics you want to run 50
ipos the initial position of the system 0.0 0.0

#TOOL=The pesmd action with label  calculates somethingpesmdLangevin dynamics on PLUMED energy landscape This action uses the defaults shown here. More details
temperature the temperature at which you wish to run the simulation in LJ units 0.722
tstep the integration timestep in LJ units 0.005
friction The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant 1
dimensionthe dimension of your energy landscape 2
nstepThe number of steps of dynamics you want to run 50
ipos the initial position of the system 0.0 0.0

plumed the name of the plumed input file containing the potential plumed.dat
idum The random number seed 0 

This file instructs pesmd to do 50 steps of Langevin dynamics on a 2D potential energy surface at a temperature of 0.722

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

plumed pesmdLangevin dynamics on PLUMED energy landscape More details --help print this help
The pesmd action with label plumed calculates something

Syntax

The following table describes the keywords that should be used in the input file for this command line tool

Keyword	Description
--help/-h	print this help
nstep	The number of steps of dynamics you want to run
temperature	the temperature at which you wish to run the simulation in LJ units
friction	The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant
tstep	the integration timestep in LJ units
dimension	the dimension of your energy landscape
plumed	the name of the plumed input file containing the potential
ipos	the initial position of the system
idum	The random number seed
periodic	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