plumed
¶
Invoke the PLUMED plugin during a MD run.
Syntax¶
This keyword has the following format:
plumed <plumed_file> <interval> <if_restart>
The plumed_file
parameter is the name of the PLUMED input file.
The interval
parameter is the interval (number of steps) of calling the PLUMED subroutines.
The if_restart
parameter determines if the PLUMED plugin should restart its calculations, which includes appending to its output files, reading the previous biases, etc.
Requirements and specifications¶
This keyword requires an external package to operate. Instructions for how to set up the PLUMED package can be found here.
Increasing the
interval
parameter will speed up your simulation if you only want PLUMED to calculate collective variables (CVs). But you have to set it to 1 if your simulation was biased by PLUMED.
Examples¶
Example 1¶
To calculate the distance between atoms, one can add:
plumed plumed.dat 1000 0
before the run command. The plumed.dat file, for example, may look like:
UNITS LENGTH=A TIME=fs ENERGY=eV
FLUSH STRIDE=1
DISTANCE ATOMS=1,2 LABEL=d1
PRINT FILE=colvar ARG=d1
The output file created by PLUMED (the colvar file) will be updated every 1000 steps.
Example 2¶
To restrain the distance between atoms, one can add:
plumed plumed.dat 1 0
before the run command. The plumed.dat file, for example, may look like:
UNITS LENGTH=A TIME=fs ENERGY=eV
FLUSH STRIDE=1
DISTANCE ATOMS=1,2 LABEL=d1
RESTRAINT ARG=d1 AT=0.0 KAPPA=2.0 LABEL=restraint
PRINT FILE=colvar ARG=d1,restraint.bias
Caveats¶
This keyword is not propagating. That means, its effect will not be passed from one run to the next.