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. |
Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients.
This action can be used to output to file biases and free energy surfaces for VES biases from previously obtained coefficients. It should be used through the driver and can only be used in post processing. The VES bias needs to be defined in the exact same way as during the simulation. At the current moment this action does not support dynamic target distributions (e.g. well-tempered).
BIAS | the label of the VES bias for to output the free energy surfaces and the bias files |
COEFFS_INPUT | the name of input coefficient file |
BIAS_OUTPUT | how often the bias(es) should be written out to file. Note that the value is given in terms of coefficient iterations. |
FES_OUTPUT | how often the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations. |
FES_PROJ_OUTPUT | how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations. |
In the following input we define a VES bias and then read in the coefficient file coeffs.input.data and output the FES and bias every 500 iterations.
phi: TORSION ATOMS=5,7,9,15 psi: TORSION ATOMS=7,9,15,17 bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi bf2: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi VES_LINEAR_EXPANSION ... ARG=phi,psi BASIS_FUNCTIONS=bf1,bf2 LABEL=ves1 GRID_BINS=100,100 PROJ_ARG1=phi PROJ_ARG2=psi ... VES_LINEAR_EXPANSION VES_OUTPUT_FES ... BIAS=ves1 FES_OUTPUT=500 FES_PROJ_OUTPUT=500 BIAS_OUTPUT=500 COEFFS_INPUT=coeffs.input.data ... VES_OUTPUT_FES
This input should be run through the driver by using a command similar to the following one where the trajectory/configuration file configuration.gro is needed to correctly define the CVs
plumed driver --plumed plumed.dat --igro configuration.gro