Reference manuals - VMD -1Petr Kulhanek kulhanek@chemi.muni.cz National Center for Biomolecular Research, Faculty of Science Masaryk University, Kotlářská 2, CZ-61137 Brno VMD Reference manuals Reference manuals - VMD -2- VMD http: //www.ks.uiuc.edu/Research/vmd/ Program for visualization of molecules. Available after free registration for MS Windows and Linux. Reference manuals - VMD -3VMD program The program is used to visualize (bio)molecules and to analyze the results of molecular dynamics simulations. The program is freely available (requires registration) and is also available for the MS Windows operating system. http://www.ks.uiuc.edu/Research/vmd/ Starting the program: $ module add vmd $ vmd Reference manuals - VMD -4Geometry optimization visualization Load xyz trajectory (optimization process) extracted by the script extract-gopt-xyz from the module qmutil into the vmd program. number of optimization steps moving between individual geometries Reference manuals - VMD -5Volumetric data Reference manuals - VMD -6Preparing volumetric data Volumetric data (cube files) can be created by the program cubegen from formatted checkpoint, which is a file containing a wave function (coefficients). Procedure: 1) preparation of formatted checkpoint 2) calculation of volumetric data 1) electron density 1) electrostatic potential $ formchk input.chk input.fchk $ cubegen 0 Density=SCF input.fchk density.cube 0 $ cubegen 0 Potential=SCF input.fchk potential.cube 0 Documentation: http://gaussian.com/g_tech/g_ur/u_formchk.htm http://gaussian.com/g_tech/g_ur/u_cubegen.htm input file from QM calculation output files for visualization formchk and cubegen are from the module gaussian. Reference manuals - VMD -7Adjustment of cube files VMD cannot load cube files created in some old versions of the gaussian program. The files must first be edited manually. Open the file in a text editor and edit it according to the instructions below. 127 -11.006092 -16.572305 -18.256495 1 107 0.333333 0.000000 0.000000 105 0.000000 0.333333 0.000000 111 0.000000 0.000000 0.333333 6 6.000000 -3.555456 -1.551346 7.591081 1 1.000000 -3.536611 -2.249523 9.541648 1 1.000000 -5.484607 -1.320526 6.909884 7 7.000000 -2.375503 0.944071 7.576727 . ........ ......... ........ ........ this number must be deleted, the rest of the file remains unchanged Reference manuals - VMD -8Visualization of volumetric data Volumetric data (cube files created by the program cubegen) can be loaded directly into the vmd program. In the default visualization, the molecule is displayed in a line model without volumetric data. Volumetric data can be displayed as (Representations): • isosurface • volumeslice Map[ping of electrostatic potential to isosurface with electron densities: 1) load the density and electrostatic potential into one molecule 2) display isosurface of the electron density 3) for isosurface, choose coloring (Coloring Method) according to volumetric data (Volume) - select the electrostatic potential, the range of colors is set in the tab Trajectory (Color Scale Data Range) Reference manuals - VMD -9Graphic representations Reference manuals - VMD -10VMD program – change of models Representation double-clicking on a line deactivates the graphical representation Reference manuals - VMD -11VMD program – change of models Selection (mask) of a part of a molecule: protein - select all amino acids water - select all water molecules chain X - select chain X resname X - select a residue named X resid X - select a residue with number X within 5 of Y - select all atoms that are 5 Å away from the atoms in Y mask not hydrogens - do not display hydrogen atoms Examples: chain A chain A B C resname ASP GLU resid 1 resid 1 to 100 within 6 of resid 100 residue can be an amino acid, ligand, or part of a ligand Reference manuals - VMD -12- Trajectories Reference manuals - VMD -13Analysis of trajectories before and after removing the translational-rotational movements beginning end every tenth frame number of frames in trajectory scroll between trajectory frames Reference manuals - VMD -14Removing TR movements Change to "all“ (all atoms), or to the part of the molecule we want to perform the superimposition to Removes the translationalrotational motion of selected atoms When evaluating the course trajectories it is advisable to remove translationalrotational (TR) motions of the whole system. This will make visual analysis of movements easier. Reference manuals - VMD -15- Measurement if we have a loaded trajectory, time course of the measured distance is displayed Reference manuals - VMD -16Histogram analysis Save to disk as a text file. File (e.g., distance.txt) contains two columns: the frame number and the measured value. $ module add cats $ histogram -c 2 distance.txt distance.hist For other setting of histogram program, see: $ histogram -h analyze the second column, i.e., the measured value