What is the recommended file format and tool for storing and visualizing anisotropic shape (ellipsoids)?

[Steven C. Howell]

I am new too HOOMD.  I am interested in using it to perform MC simulations of hard ellipsoids.  The 2013 HOOMD webinar mentions using XML and DCD files with VMD for storing and visualizing results.  Going through the documentation though, it seem outputting to XML and DCD file formats has been deprecated in favor of the new GSD file format but this does not seem to be supported by VMD.

Searching through the Google Group, I found a recent topic discussing about troubles with viewing a periodic box in VMD and another recent topic that points users to ovito for viewing GSD files.  It seems the GSD file will store the anisotropy and orientation, is this correct?  Also, will ovito display the anisotropy and orientation from a simulation trajectory?

[Joshua Anderson]

Yes, GSD stores the particle orientation (where DCD does not) - this is one of the main reasons I implemented the format. I still have not written a VMD plugin for GSD, is anyone in the community willing to step up? Everyone wants one, but I have no time to work on it for at least the next 3 months. I do understand that this is a pain point for users transitioning to hoomd's main file format.

Regardless, VMD has no ellipsoid representation to display the particles, so reading the orientation into VMD does not really help you achieve your goal. I don't see ellipsoids mentioned in a quick search of the ovito documentation either. We have an internal code that we developed to visualize particles with orientation, such as ellipsoids and polyhedra: I do not know what the rest of the HOOMD community is using.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

On Mon, Nov 7, 2016 at 4:52 PM, Steven C. Howell <steven....@gmail.com> wrote:

I am new too HOOMD.  I am interested in using it to perform MC simulations of hard ellipsoids.  The 2013 HOOMD webinar mentions using XML and DCD files with VMD for storing and visualizing results.  Going through the documentation though, it seem outputting to XML and DCD file formats has been deprecated in favor of the new GSD file format but this does not seem to be supported by VMD.

Searching through the Google Group, I found a recent topic discussing about troubles with viewing a periodic box in VMD and another recent topic that points users to ovito for viewing GSD files.  It seems the GSD file will store the anisotropy and orientation, is this correct?  Also, will ovito display the anisotropy and orientation from a simulation trajectory?

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[Steven C. Howell]

Thanks for this Josh.  I know PyMOL is able to render ellipsoids using the PDB ANISOU field.  I was trying to hack this to visualize geometric ellipsoids before I found HOOMD.  Unfortunately, this would require a full PDB frame for each trajectory step. I was hoping the GSD file would work but PyMOL could not read it.  Is it at all likely that the internal code you use for visualize will be released, either as a paid or open source application?

What do others use to visualize geometric shapes?  

On Tuesday, November 8, 2016 at 7:16:25 AM UTC-7, Joshua A. Anderson wrote:

Yes, GSD stores the particle orientation (where DCD does not) - this is one of the main reasons I implemented the format. I still have not written a VMD plugin for GSD, is anyone in the community willing to step up? Everyone wants one, but I have no time to work on it for at least the next 3 months. I do understand that this is a pain point for users transitioning to hoomd's main file format.

Regardless, VMD has no ellipsoid representation to display the particles, so reading the orientation into VMD does not really help you achieve your goal. I don't see ellipsoids mentioned in a quick search of the ovito documentation either. We have an internal code that we developed to visualize particles with orientation, such as ellipsoids and polyhedra: I do not know what the rest of the HOOMD community is using.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

On Mon, Nov 7, 2016 at 4:52 PM, Steven C. Howell <steven....@gmail.com> wrote:

I am new too HOOMD.  I am interested in using it to perform MC simulations of hard ellipsoids.  The 2013 HOOMD webinar mentions using XML and DCD files with VMD for storing and visualizing results.  Going through the documentation though, it seem outputting to XML and DCD file formats has been deprecated in favor of the new GSD file format but this does not seem to be supported by VMD.

Searching through the Google Group, I found a recent topic discussing about troubles with viewing a periodic box in VMD and another recent topic that points users to ovito for viewing GSD files.  It seems the GSD file will store the anisotropy and orientation, is this correct?  Also, will ovito display the anisotropy and orientation from a simulation trajectory?

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[Michael Howard]

The only anisotropy we do is patchy particles (Janus colloids, etc.), and for that vmd or pymol can be hacked. Drawing ellipsoids, etc. is much harder, although maybe there is a renderer out there that can do it. My time is also limited to work on a vmd plugin for at least the next 3 months, but we have some collaborators who are interested. (Right now they are converting gsd into pdb or xml after the simulation runs.) I may be able to persuade one of them to work on it, but I wouldn't say that's likely.

--Mike

[Steven Howell]

The only reason I cared about using anisotropy is PyMOL can render PDB's with ANISOU as ellipsoids.  It is just a hack to visualize ellipsoids in PyMOL.  I am not sure what it would take to get VMD to display ellipsoids or other geometric shapes.  As you say, it would also require having a plugin to read the GSD files first.  

I will check with the ovito developers to find out if they have a development plan for viewing geometric shape, other than just spheres, as they already support reading GSD files.

Steve Howell

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[Simon Schnyder]

Dear Joshua,

I was trying to visualise ellipsoids with Ovito but could not figure out where and if their anisotropic shape is saved within the GSD file format. Ovito picks up the orientation by itself but seems unable to find the shape.

I would be super thankful if you could help me out with this.

Best,

Simon

On Tuesday, November 8, 2016 at 11:16:25 PM UTC+9, Joshua A. Anderson wrote:

Yes, GSD stores the particle orientation (where DCD does not) - this is one of the main reasons I implemented the format. I still have not written a VMD plugin for GSD, is anyone in the community willing to step up? Everyone wants one, but I have no time to work on it for at least the next 3 months. I do understand that this is a pain point for users transitioning to hoomd's main file format.

Regardless, VMD has no ellipsoid representation to display the particles, so reading the orientation into VMD does not really help you achieve your goal. I don't see ellipsoids mentioned in a quick search of the ovito documentation either. We have an internal code that we developed to visualize particles with orientation, such as ellipsoids and polyhedra: I do not know what the rest of the HOOMD community is using.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

On Mon, Nov 7, 2016 at 4:52 PM, Steven C. Howell <steven....@gmail.com> wrote:

I am new too HOOMD.  I am interested in using it to perform MC simulations of hard ellipsoids.  The 2013 HOOMD webinar mentions using XML and DCD files with VMD for storing and visualizing results.  Going through the documentation though, it seem outputting to XML and DCD file formats has been deprecated in favor of the new GSD file format but this does not seem to be supported by VMD.

Searching through the Google Group, I found a recent topic discussing about troubles with viewing a periodic box in VMD and another recent topic that points users to ovito for viewing GSD files.  It seems the GSD file will store the anisotropy and orientation, is this correct?  Also, will ovito display the anisotropy and orientation from a simulation trajectory?

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