NAMD Wiki: NamdAndVEGA

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VEGA ZZ - Molecular Modeling Toolkit for Windows

VEGA ZZ is a complete molecular modelling suite for Windows that includes some features to make the NAMD use very easy:

  • full graphic user interface to control the NAMD simulation parameters (click here);
  • possibility to apply user-defined pre-settings to simplify the most common calculations (e.g. minimization, simple molecular dynamics with or without constraints, etc);
  • interactive NAMD run;
  • automatic generation of all input files required by NAMD (PDB, PSF and command file);
  • capability to save topologies (PSF files) of any type of molecule;
  • force field and atom charges attribution (click here);
  • automatic topology and parameters check in order to find missing parameters before the MD run. This features is very useful for NAMD calculations with non standard topologies (click here);
  • capability to read MD trajectories: Accelrys archive file (.arc), AutoDock 4 DLG output, BioDock output, Crystallographic Information Framework multi-model (CIF, mmCIF), CSR (Accelrys conformational search), DCD (CHARMM, NAMD), ESCHER NG, Gromacs TRR, Gromacs XTC, IFF/RIFF (32 and 64 bit), MDL Mol multi-model, Mol2 multi-model and PDB multi-model;
  • simulation trajectory visualization and animation;
  • analysis of molecular dynamics trajectory files: distances, angles, torsions, angles between two planes, dipole moment, gyration radius, ILM, MLP, lipole, PSA, RMSD, surface area, surface diameter, volume and volume diameter (click here);
  • cluster analysis of the trajectory files (cluster by coordinates, by torsion and by torsion RMSD);
  • native video compression for animations: the trajectory files can be converted in real animation files (AVI, MPEG-1 and MPEG-2) without external software. VEGA uses the Windows codecs for the standard AVI files and a built-in library to encode MPEG-1 & 2 streams. The MD animations can be converted in DVD, Super Video CD, Video CD and video streams for the Web in easy way (click here);
  • slow motion feature converting the trajectory files to video streams;
  • MD trajectory conversion: you can convert DCD files to TRR or XTC to use the Gromacs analysis tools (click here);
  • scripts for MD analysis and file manipulation (click here).

VEGA ZZ is freely available for non-profit academic use and the complete list of the implemented features is available at

MD mini how to

How to open a trajectory file

Firstly, the trajectory file must be in any format supported by VEGA ZZ (for more information, click here). Some trajectory formats need another file to be opened because they don't contain the information on atoms, residues, etc, but they have the atom coordinates only. The formats requiring an extra molecule file are: AutoDock 4 DLG, BioDock 3.0, DCD, ESCHER NG, GROMACS TRR and XTC and Quanta conformational search .csr. VEGA ZZ is able to find automatically the required file starting from the trajectory file name and changing the extension (e.g. my_trajectory.dcd -> my_trajectory.pdb). It performs changes for three times with three different file extensions (e.g. .iff, .pdb and .crd) that are typical for each trajectory format. If VEGA ZZ can't find the file, it's unable to read the trajectory. To fix the problem, the possible solutions are two: - Put the molecule file with the same file name prefix of the trajectory (see the example above) in the directory where the trajectory is present. VEGA ZZ can recognize if that file is compatible with the trajectory and if this condition is not satisfied, an error is shown. - Open the molecule file (File -> Open) that can be in any directory with any name and thus open the trajectory file (Calculate -> Analysis), clicking the open button or dragging the file over the trajectory analysis window. For AutoDock 4 DLG, BioDock 3.0 and ESCHER NG, the associated files are obtained from the record inside the trajectory file. The AutoDock 4 DLG loader, if doesn't find the file, performs the same procedure explained above as last chance.

How to remove the water molecules from a DCD file

  • open the trajectory file (File -> Open). If the associated molecule file doesn't have the same prefix (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File -> Open); 2) Open the trajectory file (Calculate -> Analysis and thus click the open button in the dialog window);
  • unselect the waters (Select -> No water);
  • save the new trajectory (File -> Save trajectory) checking Active only in the Options box.
  • to open the new trajectory, you need an appropriate coordinate file without water molecules. To do it, remove the invisible atoms (Edit -> Remove -> Invisible atoms) and save the molecule with the same name of the new trajectory file (File -> Save As...).

How to join two or more trajectory files

  • Make a copy of the first trajectory file;
  • open the second trajectory file (File -> Open). If the associated molecule file doesn't have the same prefix in the file name, read the previous section;
  • save the trajectory (File -> Save trajectory), using the format, the path and the file name of the first trajectory file. A requester will be shown: click Append. The trajectory will be joined to the end of the first one.
  • repeat the operation for each trajectory that you want join.

Trajectory format conversion

  • Open the trajectory file (File -> Open). If the associated molecule file doesn't have the same prefix in the file name, read above;
  • save the trajectory (File -> Save trajectory), choosing the new file format;
  • if you want save more disk space, you could save the trajectory in the Gromacs XTC format that uses the XDRF compression algorithm for the floating point data.

How to check the protein structure quality during a MD simulation

VEGA ZZ includes a powerful script (File -> Run script, Trajectory group, Ramachandran.c script) that can perform the Ramachandran analysis for each trajectory frame. For each frame, the Phi and Psi backbone torsion angles are measured and evaluated if they are inside or outside the Ramachandran permission areas. For each frame is calculated the percentage referred to the total number of the residues and these values are visualized in a plot. This calculation is also useful to highlight the secondary structure evolution during a MD simulation. If the percentage of the residues (Phi and Psi values) inside the permission areas is decreasing during the simulation, it means that the secondary structure evolves to a worse situation. Vice versa, if the percentage is growing, the secondary structure is improving. Warning: before to run the script, you must open a trajectory file.