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Visualising a system with graphene

  1. Nov 4, 2015 #1
    I am currently modelling van der Waals interactions using DFT-D as my undergrad thesis. The basic set-up is a molecule suspended above a crystal surface. To start the surface is graphene, which has been causing me some trouble as neither VMD nor VESTA are allowing me to visualise the set-up correctly from the POSCAR. I need to visualise the system so that I can move the molecule above the surface into a variety of positions as well as duplicate it in preparation for modelling in VASP. However when performing these operations in VMD I run into the known problem that the graphene is rotated and deformed whenever I try to save and then re-open the POSCAR on account of its non-cubic structure. VESTA on the other hand is completely unable to read the POSCAR file, though VMD can at least do that without complaint. At the moment I am forced to manipulate the File manually, but this is eating up valuable project time. Has anybody else experienced similar issues when manipulating graphene in VMD or VESTA, and if so, what did you do to get around these issues?
  2. jcsd
  3. Nov 6, 2015 #2
    I'm also an undergrad who's done some DFT work with graphene molecules (well, benzene, naphthalene, etc. up to Circumbiphenyl). I don't have the experience modeling graphene in VMD or VESTA, but I did somewhat similar operations using Avogadro and/or Gabedit. Rotating the structure and copying it wasn't a big deal (except for when it tried to automatically make bonds where there shouldn't have been any), and it worked well enough. Maybe you can look into those. But those are for finite graphene molecules, if you want to consider an 'infinite' graphene sheet (using periodic DFT codes), then I can't help you there.
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