ves_md_linearexpansion

This is part of the ves module | |

It is only available if you configure PLUMED with ./configure –enable-modules=ves . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |

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

\[ U(x,y) = x^4 + y^4 - 2 x^2 - 4 y^2 + xy + 0.3 x + 0.1 y \]

To define the potential we employ polynomial power basis functions (BF_POWERS). The input file is given as

nstep 10000 tstep 0.005 temperature 1.0 friction 10.0 random_seed 4525 plumed_input plumed.dat dimension 2 replicas 1 basis_functions_1 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0 basis_functions_2 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0 input_coeffs pot_coeffs_input.data initial_position -1.174,+1.477 output_potential potential.data output_potential_grid 150 output_histogram histogram.data # Wolfe-Quapp potential given by the equation # U(x,y) = x**4 + y**4 - 2.0*x**2 - 4.0*y**2 + x*y + 0.3*x + 0.1*y # Minima around (-1.174,1.477); (-0.831,-1.366); (1.124,-1.486) # Maxima around (0.100,0.050) # Saddle points around (-1.013,-0.036); (0.093,0.174); (-0.208,-1.407)

This input is then run by using the following command.

plumed ves_md_linearexpansion input

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

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

p:POSITIONATOM=1the atom number.ene:ENERGY PRINTARG=the input for this action is the scalar output from one or more other actions.p.x,p.y,eneFILE=colvar.datathe name of the file on which to output these quantitiesFMT=%8.4fthe format that should be used to output real numbers

- Glossary of keywords and components

- Compulsory keywords

nstep | ( default=10 ) The number of steps of dynamics you want to run. |

tstep | ( default=0.005 ) The integration timestep. |

temperature | ( default=1.0 ) The temperature to perform the simulation at. For multiple replica you can give a separate value for each replica. |

friction | ( default=10. ) The friction of the Langevin thermostat. For multiple replica you can give a separate value for each replica. |

random_seed | ( default=5293818 ) Value of random number seed. |

plumed_input | ( default=plumed.dat ) The name of the plumed input file(s). For multiple replica you can give a separate value for each replica. |

dimension | ( default=1 ) Number of dimensions, supports 1 to 3. |

initial_position | Initial position of the particle. For multiple replica you can give a separate value for each replica. |

replicas | ( default=1 ) Number of replicas. |

basis_functions_1 | Basis functions for dimension 1. |

input_coeffs | ( default=potential-coeffs.in.data ) Filename of the input coefficient file for the potential. For multiple replica you can give a separate value for each replica. |

output_coeffs | ( default=potential-coeffs.out.data ) Filename of the output coefficient file for the potential. |

output_coeffs_fmt | ( default=%30.16e ) Format of the output coefficient file for the potential. Useful for regtests. |

output_potential_grid | ( default=100 ) The number of grid points used for the potential and histogram output files. |

output_potential | ( default=potential.data ) Filename of the potential output file. |

output_histogram | ( default=histogram.data ) Filename of the histogram output file. |

- Options

`--help/-h` | ( default=off ) print this help |

basis_functions_2 | Basis functions for dimension 2 if needed. |

basis_functions_3 | Basis functions for dimension 3 if needed. |

coeffs_prefactor | prefactor for multiplying the coefficients with. For multiple replica you can give a separate value for each replica. |

template_coeffs_file | only generate a template coefficient file with the filename given and exit. |