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Detecting micro domains in model membranes with APL@VORO

1/26/2015

APL@Voro is a program developed to aid in the analysis of Molecular dynamics trajectories of lipid bilayer simulations. Initially designed to work with GROMACS trajectory files, it may be used also with other trajectories if they are converted to Gromacs format (needed are the Gromacs trajectory file, PDB coordinate files and a GROMACS index files) to create a two dimensional geometric representation of a bilayer. The analysis of the bilayer is supported by using the Voronoi diagrams and Delaunay triangulations generated for different selection models of lipids. The values calculated on the geometric structures can be visualized in an interactive environment, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins and calculates the area per lipid and the bilayer thickness. The program is written in C++, open source and published under the GPL 3.0 License.

Download the software here.

For the algorithms used click here.

136 Comments

VMD analysis plugins for membrane simulations

10/10/2013

4 Comments

MEMBPLUGIN http://sourceforge.net/p/membplugin/wiki/Home/

Diffusion Coefficient Tool http://multiscalelab.org/utilities/DiffusionCoefficientTool

VMD Density Profile Tool http://multiscalelab.org/utilities/DensityProfileTool

George

4 Comments

Visualize an trajectory created by Impact (Schrodinger)

3/11/2013

0 Comments

To visualize an impact trajectory, open the panel with the Impact parameters before starting the run and click on "Record Trajectory", which is deselected by default. The option is under: Applications -> Impact -> Dynamics -> MD Parameters -> Record Trajectory".
After your trajectory is ready, you will see a "T" in your project table. Click on the "T" and a trajcetory viewing panel will open.

To prepare a video file for incorporation into PowerPoint showing your modelling results you can use the following options:

You can create a movie in MPEG format of the selected entries in the Project Table with Entry → Record Movie.
From Suite 2010 on you can create a movie in MPEG format of a sequence of Workspace views, by clicking Record Movie in the Manage Views panel.
You can record a movie of a Desmond (or Impact) trajectory, in the Trajectory panel.
You can use the Maestro Viewer ActiveX control in a PowerPoint presentation, to show a structure in a Maestro window, and manipulate it (rotate, translate, zoom) in the presentation.

See also:

http://www.schrodinger.com/kb/354

Zoe

0 Comments

Contact Module in Maestro - contact cutoff ratio

11/30/2012

1 Comment

In Maestro when visualizing a structure file, you can select Tools -> Measurements -> Contacts panel in order to see Good contacts and Bad&Ugly contacts. When contacts are displayed, good contacts are green by default, bad ones are orange, and ugly ones are red. These criteria whether a contact is defined as good, bad or ugly are based on the following formula:

C = D12 / ( R1 + R2 )

where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the radii of atomic centers 1 and 2. C is defined as the "contact cutoff ratio" in Maestro and has default values of 0.85 for "Bad" contacts and 0.70 for "Ugly" contacts. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). These three values then provide 4 ranges. Distances greater than C(good) are not marked, less than C(good) but greater than C(bad) are marked as "good", etc.

This answer was provided by the Schrodinger help team.

Zoe

1 Comment

Analysis of MD simulations using GROMACS tools

11/7/2012

5 Comments

I just came across this presentation which very nicely summarises the most important analysis tools for proteins available in Gromacs: Definitely worth reading and very good as a reference for experienced gromacs users.

Analysis tools that you can find in the presentation include:
- Looking at your trajectory
- Groups in analysis
- Root mean square deviations and fluctuations
- Radius of gyration and distances
- Hydrogen bonds
- Secondary structure analysis
- Free energy surfaces
- Principal component analysis: using Cartesian coordinates or dihedral angles
- Clustering

Evi

5 Comments

Detecting micro domains in model membranes with APL@VORO

VMD analysis plugins for membrane simulations

Visualize an trajectory created by Impact (Schrodinger)

Contact Module in Maestro - contact cutoff ratio

Analysis of MD simulations using GROMACS tools

Alexis, Maria, Michalis, Danai, Panos, Eirini, Sotiris, Nastazia, Matilde, Zoe

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