VMD selections#

This file: VMD has very powerful tools for selecting atoms and molecules based on a number of different criteria. Below is a brief summary.

Keywords: VMD, VMD Plugins, visualization, atomistic simulations

Associated material:

VMD 1UBQ

Name, residue etc.-based selection#

COMMAND

EXPLANATION

name CA

select all \(\alpha\)-carbons

name CA and resname ALA

select all \(\alpha\)-carbons in ALA residues

resid 35

select residue 35

resid 35 to 40

select residues 35–40

backbone not protein

select protein backbone atoms

name "C.*"

select all carbon atoms

Distance-based selection#

Note: In VMD distances are measured in Å. In Gromacs, for example, distances are measured in nanometers.

COMMAND

EXPLANATION

z < 6 and z > 3

select atoms that are between 3 and 6 Å in the z-coordinate

within 5 of name FE

select atoms that are within 5 Å of iron atoms

protein within 5 of nucleic

select atoms that belong to proteins and are within 5 Å from nucleic acids

water within 3 of protein

select water molecules that are within 3 Å from a protein

Mass-based selection#

COMMAND

EXPLANATION

mass < 5

select atoms that are not heavier than 5 a.u.

Charge-based selection#

COMMAND

EXPLANATION

abs(charge) > 1

select atoms with a net charge larger than 1

Bond-based selection#

COMMAND

EXPLANATION

numbonds = 2

select atoms that are bonded to 2 other atoms (= have 2 bonds)

Selection in one frame vs in every frame of a trajectory#

To have the selection update for every frame, select

Graphics -> Graphical Representations -> Trajectory -> Update Selection Every Frame

Periodic boundaries: Lines/bonds all over the place#

  • Atoms are bonded across periodic boundary conditions (PBC).

  • Trajectory post-processing is required to make molecules whole.

More information#

https://docs.computecanada.ca/wiki/VMD