Command line tool: ves_md_linearexpansion
| Module | ves |
|---|---|
| Description | Input |
| MD of a one particle on a linear expansion PES | file |
Details
Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.
This is simple MD code that allows running dynamics of a single particle on a potential energy surface given by some linear basis set expansion in one to three dimensions.
It is possible to run more than one replica of the system in parallel.
Examples
In the following example we perform dynamics on the Wolfe-Quapp potential that is defined as
This function has minima at (-1.174,1.477); (-0.831,-1.366); (1.124,-1.486), a maxima at (0.100,0.050) and saddle points around (-1.013,-0.036); (0.093,0.174); (-0.208,-1.407).
To define the potential we employ polynomial power basis functions (BF_POWERS). The input file is given as
#TOOL=ves_md_linearexpansionMD of a one particle on a linear expansion PES This action has hidden defaults. More details nstep The number of steps of dynamics you want to run 10000 tstep The integration timestep 0.005 temperature The temperature to perform the simulation at 1.0 friction The friction of the Langevin thermostat 10.0 random_seed Value of random number seed 4525 plumed_input The name of the plumed input file(s) plumed.dat dimension Number of dimensions, supports 1 to 3 2 replicas Number of replicas 1 basis_functions_1Basis functions for dimension 1 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0 basis_functions_2Basis functions for dimension 2 if needed BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0 input_coeffs Filename of the input coefficient file for the potential pot_coeffs_input.data initial_positionInitial position of the particle -1.174,+1.477 output_potential Filename of the potential output file potential.data output_potential_grid The number of grid points used for the potential and histogram output files 150 output_histogram Filename of the histogram output file histogram.data
This input is then run by using the following command.
plumed ves_md_linearexpansionMD of a one particle on a linear expansion PES More details
The corresponding pot_coeffs_input.data file is
#! FIELDS idx_dim1 idx_dim2 pot.coeffs index description
#! SET type LinearBasisSet
#! SET ndimensions 2
#! SET ncoeffs_total 25
#! SET shape_dim1 5
#! SET shape_dim2 5
0 0 0.0000000000000000e+00 0 1*1
1 0 0.3000000000000000e+00 1 s^1*1
2 0 -2.0000000000000000e+00 2 s^2*1
4 0 1.0000000000000000e+00 4 s^4*1
0 1 0.1000000000000000e+00 5 1*s^1
1 1 +1.0000000000000000e+00 6 s^1*s^1
0 2 -4.0000000000000000e+00 10 1*s^2
0 4 1.0000000000000000e+00 20 1*s^4
#!-------------------
One then uses the (x,y) position of the particle as CVs by using the POSITION action as shown in the following PLUMED input
p: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1 ene: ENERGYCalculate the total potential energy of the simulation box. More details PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p.x,p.y,ene FILEthe name of the file on which to output these quantities=colvar.data FMT the format that should be used to output real numbers=%8.4f
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 |
| tstep | The integration timestep |
| temperature | The temperature to perform the simulation at |
| friction | The friction of the Langevin thermostat |
| random_seed | Value of random number seed |
| plumed_input | The name of the plumed input file(s) |
| dimension | Number of dimensions, supports 1 to 3 |
| initial_position | Initial position of the particle |
| replicas | Number of replicas |
| basis_functions_1 | Basis functions for dimension 1 |
| basis_functions_2 | Basis functions for dimension 2 if needed |
| basis_functions_3 | Basis functions for dimension 3 if needed |
| input_coeffs | Filename of the input coefficient file for the potential |
| output_coeffs | Filename of the output coefficient file for the potential |
| output_coeffs_fmt | Format of the output coefficient file for the potential |
| coeffs_prefactor | prefactor for multiplying the coefficients with |
| template_coeffs_file | only generate a template coefficient file with the filename given and exit |
| output_potential_grid | The number of grid points used for the potential and histogram output files |
| output_potential | Filename of the potential output file |
| output_histogram | Filename of the histogram output file |