Notes on some use­ful VMD tips


In this note, I will ac­cu­mu­late some VMD tips I find use­ful. The main pur­pose of this note is for self con­ve­nience but I hope it can be use­ful for any­one who wan­der on this page

How to gen­er­ate VMD .psf file from LAMMPS data file

In VMD con­sole, use com­mand cd to nav­i­gate to the di­rec­tory where the LAMMPS data file is lo­cated. Then, run the fol­low­ing com­mand

topo readlammpsdata your_data_file bond
animate write psf your_psf_file

If the com­mand runs suc­cess­fully, then you should find your .psf file gen­er­ated in the di­rec­tory. To use the .psf file, first load the gen­er­ated .psf file and then load the tra­jec­tory file. You should find your­self be able to use the func­tion­al­i­ties such as draw­ing method, col­or­ing method, etc …

Fix cer­tain mol­e­c­u­lar in the cam­era when view the tra­jec­tory file

Sometimes, we want to view cer­tain mol­e­c­u­lar through the tra­jec­tory. However, the tar­geted mol­e­c­u­lar may dif­fuse in the sim­u­la­tion box, mak­ing the vi­su­al­iza­tion dif­fi­cult. We want to make the cam­era fo­cus on the in­ter­ested mol­e­c­u­lar. Here is a method to do this.

In Extension-Analysis-RMSD Visualizer Tool, use mol­e­c­u­lar you want to fo­cus on as Atom Selection. Then run ALIGN. You can watch the tra­jec­tory as the mol­e­c­u­lar you se­lect in the cen­ter of the cam­era now.

Rendering for pub­li­ca­tion qual­ity im­age

To ren­der pub­li­ca­tion qual­ity im­age, fol­low the good prac­tices be­low

  • Load mol­e­c­u­lar into VMD with your pre­ferred rep­re­sen­ta­tion
  • For each rep­re­sen­ta­tion, se­lect a ma­te­r­ial that is fairly dif­fuse such as the Diffuse ma­te­r­ial, or the AO-optimized AOShiny, AOChalky, or AOEdgy ma­te­ri­als pro­vided in VMD.
  • Enable am­bi­ent oc­clu­sion light­ing in the Display Settings win­dow as de­scribed above.
  • Set the AO Ambient fac­tor to 1.0, and the AO Direct fac­tor to 0.8 as an ini­tial start­ing point.
  • Render the scene us­ing File - Render - Tachyon or TachyonInternal, or use the render com­mand to do the same.
  • Due to the in­creased com­pu­ta­tional com­plex­ity of ren­der­ing the mol­e­cule with am­bi­ent oc­clu­sion light­ing, it’s highly rec­om­mended to run VMD and Tachyon on a multi-proces­sor or multi-core work­sta­tion for best per­for­mance.

References