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11 votes

How to include individual PBC box dimensions in xyz file format compatible with VMD

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 ...
Camps's user avatar
  • 22.9k
10 votes

Molecular dynamics frame distorted by VMD?

Don't Worry, it is not a problem, This happened because you used PBC (Periodic boundary condition) and VMD sometimes has bugs during the visualization in this case. The most important to you to see ...
Abd-Elazeem Mohamed's user avatar
9 votes
Accepted

How do I build and run a simulation of water molecules in NAMD?

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 ...
Camps's user avatar
  • 22.9k
9 votes
Accepted

Can VMD change its cartoon representation for secondary structure according to trajectories?

Yes, It can. Just run this script in Extensions --> TK console of vmd before visualizing ...
Vasista's user avatar
  • 1,291
8 votes
Accepted

How to assign "Trajectory Smoothing Window Size" inside VMD Tcl script

You could use mol smoothrep x y z where x is the molid y...
Vasista's user avatar
  • 1,291
8 votes
Accepted

Recalculate atom positions to account for periodic boundary conditions

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 ...
Fabian's user avatar
  • 1,401
8 votes

File type to write bond information

In the VMD user guide different file formats natively handled by VMD are specified, including PSF and PARM that can both contain ...
Hebo's user avatar
  • 1,665
7 votes
Accepted

How do I use a LAMMPS initial data file in VMD to see the material structure?

Topotools plugins does provide you a method to read LAMMPS native data files. See the documentation for detailed usage. For instance, if the file data.CNT contains ...
Seyed Mohamad Moosavi's user avatar
7 votes

File type to write bond information

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 ...
WaterMolecule's user avatar
7 votes
Accepted

How to visualize protein-ligand complex MD run using VMD

First, You need to click on Create Rep and you will get a new line in the box below as the picture attached (with the same name "protein" in your case). To show the ligand, you should know ...
Abd-Elazeem Mohamed's user avatar
7 votes
Accepted

Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition

When you are doing an MD simulation, you should ideally be using a large simulation box so that you can study the properties of the system. However, this is easier said than done because of the ...
Hemanth Haridas's user avatar
6 votes

Secondary structure information at each frame in a VMD trajectory

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 ...
Roni Saiba's user avatar
6 votes

How to include individual PBC box dimensions in xyz file format compatible with VMD

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 ...
Fabian's user avatar
  • 1,401
6 votes
Accepted

Calculating RMSF in VMD

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 ...
Roni Saiba's user avatar
6 votes

Extracting bond information from the xyz positions of atoms?

This seems to be what the TopoTools plugin is used for. This has commands for manipulating bonds/angles/dihedrals in VMD and then writing the corresponding information to a LAMMPS input file.
6 votes

Limits of periodic box from pdb

Atomic simulation environment is useful for a lot of other manipulations you might want to do and it comes with a GUI that is capable of doing this (given that you define the cell, it will also behave ...
Tristan Maxson's user avatar
6 votes

How to study the stability of structure in water and analyze the radial distribution function (RDF)?

Here are my two cents (things that I would try): How can I confirm the stability of the micelle? You could run the simulation for a longer time and/or run at different temperatures. Also, monitoring ...
Camps's user avatar
  • 22.9k
6 votes

How to visualize a slice of the unit cell?

I recently used OVITO for this same visualization. There is an option, Slice, within the quick command search that is available in the free version. You can use it ...
T. A.'s user avatar
  • 113
5 votes

How to apply colors and graphics to VMD from Tcl?

Take a look at the options in the Menu --> File --> Log Tcl Commands to File:
Camps's user avatar
  • 22.9k
5 votes
Accepted

Limits of periodic box from pdb

In pymol the cell can be displayed by typing show cell into the command line.
AwakenYesterday's user avatar
5 votes

How to show orientation axis in Pymol

As far as I know, there is no built in way to display the coordinate vectors. Fortunately, on the PyMOLWiki I was able to find a page with a number of scripts you can use to do this.
AwakenYesterday's user avatar
5 votes
Accepted

How to generate CNT bond-type information for LAMMPS intial file?

Use Tkconsole under extension and follow topo retypebonds topo guessdihedrals topo writelammpsdata lmp.data full
Pranav kumar's user avatar
  • 3,969
5 votes

Recalculate atom positions to account for periodic boundary conditions

You can use ATOMSK. The command: atomsk initial.xyz -wrap final.xyz will wrap all the atom coordinates back into your simulation box. ...
Sufyan's user avatar
  • 633
5 votes

VMD polymer draws multiple bonds

You have provided a LAMMPS data file as input to VMD and AFAIU, the default New Molecule option from VMD can't read this format. I am not sure how you are reading ...
Rashid Rafeek's user avatar
4 votes
Accepted

Molecular dynamics frame distorted by VMD?

Its neither a biophysical effect nor a bug in your MD simulation steps. It's just an visualisation issue. You could use the gmx trjconv command to make your protein ...
Vasista's user avatar
  • 1,291
4 votes
Accepted

How to add a bond between two atoms in VMD?

topo addbond x y should do the trick. where x is the index of the atom of an residue in which you are interested. if you want a more automated way, then you need to ...
Vasista's user avatar
  • 1,291
4 votes
Accepted

Merging multiple PDB files in VMD using Tcl scripts?

...
Vasista's user avatar
  • 1,291
4 votes
Accepted

VMD Periodic boundary wrapping using pbc wrap

If you need to wrap a simulation trajectory using VMD, and want to ensure that the molecules remain as is (and no artifacts are introduced) use the following command: ...
Hemanth Haridas's user avatar
4 votes
Accepted

Write full box to topology file + script representation

As per documentation (search for "molid"), TopoTools only works on one "VMD molecule" at a time, and by default this is just mol top. Your ...
Shern Ren Tee's user avatar
3 votes

What package do I use to model a material and get the LAMMPS data file as an output?

First, can you clarify what you mean by "it explodes"? Have you ensured that there are no overlaps in your simulation and that the force-field parameters are correct? Moltemplate is another ...
Ardalan's user avatar
  • 101

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