13
$\begingroup$

I am looking for a list of programs that support structure relaxations via molecular mechanics (e.g. via UFF) with the following conditions:

  1. The program is free (free with an academic license is okay)
  2. It works on materials with periodic boundary conditions
  3. It can read/write CIF
  4. It has a GUI
  5. It supports automatic bond-typing that can be adjusted via the GUI if desired

An example of a commercial program that can do this is Materials Studio. I'm looking for free alternatives, however.

Improve this question
$\endgroup$
13
  • 2
    $\begingroup$ +1 I see this becoming another valuable list that will also help a lot of future users too! Thanks for the good question! $\endgroup$
    – Nike Dattani - No Free Time
    Commented Apr 9, 2021 at 2:52
  • 2
    $\begingroup$ Avogadro fulfills most of them. I believe it can handle pbc, but I am not completely sure. $\endgroup$
    – S R Maiti
    Commented Apr 9, 2021 at 9:17
  • $\begingroup$ is this for small molecules, or proteins? The requirement for PBC suggests some kind of simulation box, so are you also looking for relaxation of water molecules? $\endgroup$
    – lewiso1
    Commented Apr 13, 2021 at 6:17
  • 1
    $\begingroup$ @ShoubhikRMaiti -- Thanks for your reply. Unfortunately, the support for PBCs is among the most important since I am interested in crystalline materials. There are several great options for molecules out there, including Avogadro and others. $\endgroup$
    – Andrew Rosen
    Commented Apr 19, 2021 at 2:04
  • 1
    $\begingroup$ Suffice to say that I’ll add an answer to the question when Avo2 can meet the needs here. $\endgroup$
    – Geoff Hutchison
    Commented May 5, 2021 at 2:22

1 Answer 1

Reset to default
7
$\begingroup$

GDIS

I think GDIS accomplishes your conditions. As it is an interface (like Material Studio) you will need to install some packages to run the tasks. As you are interested in using molecular mechanics (with UFF), I recommend to install also the GULP package, specialized in molecular dynamics and in lattice dynamics.

GDIS is a GTK based program for the display and manipulation of isolated molecules and periodic systems. It is in development, but is nonetheless fairly functional.

It has the following features:

  • Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
  • OpenGL rendering (requires gtkglarea)
  • Assorted tools for visualization (measurements, ribbons, polyhedral display)
  • Useful manipulation tools, including matrix transformations and periodic image display.
  • Powerful surface generation and crystal morphology tools.
  • Animation of BIOSYM and GULP trajectory files

GDIS also allows you to perform the following functions through other packages:

  • Model rendering (courtesy of POVRay)
  • Energy minimization (courtesy of GULP)
  • Morphology calculation (courtesy of cdd)
  • Space group processing (courtesy of SgInfo)
  • View the Periodic Table (courtesy of GPeriodic)
  • Load additional filetypes, such as PDB (courtesy of Babel)

Site: http://gdis.seul.org/

Improve this answer
$\endgroup$

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .