Analyze TINKER structures

The analyze program of TINKER implements many different king of analysis on molecular structures:

  • Total potential Energy and its component [E]
  • Energy Breakdown over each of the atoms [A]
  • List of the large individual interactions [L]
  • Details for all individual interactions [D]
  • Electrostatic, Inertial & Virial properties [M]
  • Force field parameters for interactions [P]

The results of those analysis depend also from the way we describe the system in the key file. A practical example is the case of a molecular self-assembly adsorbed on surface. With this system, the standard use of analyze with the option E will give as intermolecular energy the sum of the molecule-molecule and molecule-surface interactions.

Let's suppose we are interested in get the energy of intermolecular interactions in the monolayer alone, i.e. without the contribution of the molecule-surface interactions. A way to influence the result of analyze is to play with the GROUP and INACTIVE keywords. Let's suppose the first 2000 atoms in the structures are the surface atoms, while the other 1540 are the atoms in the monolayer. In order to get the energy of intermolecular interactions in the monolayer alone, the key file need to be modified as below:

group 1   -1      2000
group 2   -2001 3540
inactive   -1      2000

Now group 1 contains all the surface atoms, while group 2 contains the atoms that are in the monolayer. With the GROUP-INTRA keyword we ask to calculate the energy that is coming from the interactions of atoms that are inside the same groups, while is neglected the energy coming from the interactions between atoms that are in different groups. This means there is no energy coming out from molecule-surface interactions. Since all the atoms in the group 1 (surface atoms) are inactive, their interaction energy is zero. That means that the only energy we are going to have is coming from the monolayer alone, and the intermolecular energy is the molecule-molecule interactions inside the monolayer.

In the same way, if we are interested in the adsorption energy of the monolayer, i.e. the energy coming from molecule-surface interactions, we can obtain it modifying the key file as following:

group 1   -1      2000
group 2   -2001 3540

This time we use the keyword GROUP-INTER to calculate the energy from the group 1-group 2 interaction, i.e. the surface-monolayer interaction, as requested.

It is important to stress the fact that we can do all these different analysis without modify the molecular structures, but simply modifying the way the system is described in the key file. Also, be aware of the fact that inactive atoms are not included in any TINKER trajectory file (.arc files) (see troubleshooting section in the main page of TINKER WIKI).

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