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5. print the content of ’e2edist’ and ’comdist’ in the file COLVAR
In the above input we have used to different ways of writing the atoms used in COM calculation:
1. ATOMS=1,2,3,4,5,6 is the explicit list of the atoms we need
2. ATOMS=251-256 is the range of atoms needed
ranges of atoms can be defined with a stride which can also be negative:
1. ATOMS=from,to:by (i.e.: 251-256:2)
2. ATOMS=to,from:-by (i.e.: 256-251:-2)
Now by plotting the content of the COLVAR file we can compare the behaviour in this trajectory of both the terminal
carbons as well as of the centre of masses of the terminal residues.
gnuplot
What do you expect to see now by looking at the trajectory? Let’s have a look at it
vmd template.pdb trajectory-short.xyz
Virtual atoms can be used in place of standard atoms everywhere an atom can be given as input, they can also be
used together with standard atoms. So for example we can analyse the TORSION angle for a set of Virtual and
Standard atoms:
first: COM ATOMS=1-6
last: COM ATOMS=251-256
cvtor: TORSION ATOMS=first,102,138,last
PRINT ARG=cvtor STRIDE=1 FILE=COLVAR
ENDPLUMED
The above CV don’t look smart to learn something about the system we are looking at. In principle CV are used to
reduce the complexity of a system by looking at a small number of properties that could be enough to rationalise its
behaviour.
Now try to write a collective variable that measures the Radius of Gyration of the system: GYRATION.
NOTE: if what you need for one or more variables is a long list of atoms and not a virtual atom one can use the
keyword GROUP. A GROUP can be defined using ATOMS in the same way we saw before, in addition it is also
possible to define a GROUP by reading a GROMACS index file.
ca: GROUP ATOMS=9,16,31,55,69,90,102,114,124,138,160,174,194,208,224,238
Now ’ca’ is not a virtual atom but a simple list of atoms.
10.1.4.3
MULTICOLVAR
Sometimes it can be useful to calculate properties of many similar collective variables at the same time, for example
one can be interested in calculating the properties of the distances between a group of atoms, or properties linked
to the distribution of the dihedral angles of a chain and so on. In PLUMED2 this kind of collective variables fall under
the name of MULTICOLVAR (cf. MultiColvar Documentation.) Here we are going to analyse the distances between
CA carbons along the chain:
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