![vmd tutorial vmd tutorial](https://i.ytimg.com/vi/7ZqR137nOe0/hqdefault.jpg)
VMD inevitably ends up displaying a cloud of dots, which are hard (impossible?) to properly visualize with non-bionic human eyes. When a CG structure/trajectory is opened with VMD, the program builds a network of bonds using a distance criteria and an atomistic library of possible bond lengths (dened by the namd forceeld, developed by the same group) CG beads, linked with bonds with an average length of 0.35 nm, are not defined through this automatic algorithm. CG bonds/constraints and elastic networks vmd file and manually add the lines you wrote to generate them at the bottom. This file contains the Tcl commands needed to obtain the current display lists of bonds and drawings (cylinders) are not saved, but you can open this. Keep in mind that you can save the visualizing state of your system whenever you want by saving a state.vmd file. And as we are simulating bigger and bigger systems in which more and more beads are involved, the previous trick can be adapted to increase the displaying/seeking speed of trajectories by writing representations showing only beads needed for the visualization (head groups of a bilayer for instance). Try it yourself! VMD is really demanding in term of memory an easy trick to decrease the amount needed by VMD is to load structure/trajectories containing only beads needed by your analysis this can easily be done by preprocessing the trajectory using trjconv.
![vmd tutorial vmd tutorial](https://technowikis.com/sites/technowikis.com/uploads/137/13708772335006701410.png)
More general keywords are implemented to be able to display non-classical-systems (CG systems are part of this second category) you can find them in VMD manual:
![vmd tutorial vmd tutorial](https://i.pinimg.com/originals/e6/7a/74/e67a748b1247af9b1827230adcdfd1b8.jpg)
VMD comes with implemented keywords for all-atom systems ("protein", "chain", "hydrogen", "solvent", etc.). VMD adopted a representation-philosophy: for any set of atoms/molecules/protein chains we want to display or analyze, we need to select this set through a "representation" defined by keywords related to this set (somewhat similar to make_ndx). A good tutorial for Bendix can be found here: Additionally, Tcl scripts are presented that assist with the visualization of CG systems these scripts, as well as extended help, are available on the Martini websiteĪn additional, very usefull tool for displaying CG (Martini) structures in VMD is Bendix. In this module, we explain some of the vmd commands that can be used to visualize the CG systems. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Martini tutorials: visualizing Martini systems using VMD