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11

That is a modification of the standard XYZ file format and is called extended XYZ format, and not all programs are compatible with it. From the VMD Molfile Plugin Documentation page, it looks that VMD is only compatible with standard XYZ format. Also, take a look at this answer (to another question) about adding PBC info in VMD after loading standard XYZ ...


9

Yes, It can. Just run this script in Extensions --> TK console of vmd before visualizing proc structure_trace {name index op} { vmd_calculate_structure $index } trace variable vmd_frame w structure_trace


8

To visualize the trajectory you can use VMD and use its pbctools vmd trajectory.xyz > pbc set {a b c alpha betta gamma} -all > pbc wrap where a, b, and c are the lattice vectors and alpha, beta, and gamma the angles. The angles can be omitted if the box is orthorhombic. For more information see here: https://www.ks.uiuc.edu/Research/vmd/plugins/...


8

In the VMD user guide different file formats natively handled by VMD are specified, including PSF and PARM that can both contain bond connectivity: PSF and PARM files contain atoms, residues, segment names, residue types, atomic mass and charge, and the bond connectivity. Depending on how your atoms and bonds are represented in python, you may choose to ...


7

I usually use mol2 or psf formats to explicitly include bonds. mol2 works with many other programs (Avogadro, OpenBabel), while psf files are good for anything in CHARMM world (CHARMM, NAMD). The psf capabilities of VMD are good since it lives in CHARMM world as well.


6

Camps is correct, VMD cannot directly parse the comment line of an xyz file because the extended ASE format is not recognized. You can, however, use a tcl-script to load the file and parse the comment line yourself. I am no tcl expert but here is an example that works for me: set filename [lindex $argv 0] # load the coordinates into vmd mol new $...


6

I have found the solution to the problem. One needs to use the animate command to change the frame in the top molecule in VMD. The corrected script which produces the desired output is as follows: set outfile [open ./percent_helix.dat w] set lookup {H G I} set frame_num [molinfo top get numframes] set full [atomselect top "name CA"] set len [...


6

The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely match the values one gets from the inbuilt function. In any case, calculating RMSF for just the C alpha atoms gives more information about the structural changes ...


5

You can use ATOMSK. The command: atomsk initial.xyz -wrap final.xyz will wrap all the atom coordinates back into your simulation box. initial.xyz is your input file and final.xyz is the output after wrapping all atoms back into the simulation box. You can get the output in many different formats. ATOMSK is quite powerful and simple to use. Please have a look ...


4

One way could be as follow. Download software PACKMOL. Download the examples files (tar.gz or zip). Modify the file solvprotein-comment.inp: removing the info about the protein, and the ions and define the number of water molecules and the size of the droplet: # # Protein solvated by water and ions # # All atoms from diferent molecules will be at least 2....


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