Questions tagged [vmd]
Questions about the Visual Molecular Dynamics (VMD) structure visualization program.
42 questions
1 vote
1 answer
109 views
How to create a PSF file for simple molecular structure that is custom made?
For a particular problem I have to do a MD simulation of a hypothetical Carbon chain molecule, made of a linear connection of 5 Carbon atoms: ...
- 323
4 votes
1 answer
152 views
Interface between Material studio and LAMMPS
How can I utilize output files (XYZ format) from LAMMPS in Materials Studio? How can I calculate the UV-visible spectrum in Materials Studio using the XYZ format extracted from LAMMPS software? Is ...
5 votes
1 answer
296 views
VR movies generation using VMD
I am trying to generate 3D/VR movies using VMD and I am having trouble. While following the general instructions here: https://www.ks.uiuc.edu/Research/vmd/minitutorials/vrmovies/ , I can set the ...
5 votes
0 answers
72 views
How to draw periodic bonds in Visual Molecular Dynamics (VMD)?
I have the LAMMPS DUMP file of a salt solution, and I am investigating the Oligomerization of the salt ions in solution. However, when I am trying to visualize the trajectory, I can only draw bonds ...
- 5,316
4 votes
0 answers
101 views
How to create a water droplet (half-sphere) on a rock (quartz) surface
I am to Equilibrate a uniformly distributed spc water molecules at 300k in 50x50x50 box. Water density is taken to be 1000kg/m3. Simulate the system in the NVT ensemble. The spc water is modeled using ...
5 votes
2 answers
591 views
How to visualize a slice of the unit cell?
I have a cell that contains a sphere of organic molecules in a cube of water. What tool and how could I visualize the central cut (slice) of the unit cell? Similar to the one visualized in packmol ...
- 1,668
4 votes
2 answers
471 views
Visualising the spatial distribution of water structure using VMD
I am trying to recreate Fig. 5b of this paper I have a solvated NH4+ in my system and would like to create a similar visualisation for my case. Can this be generated using VMD? If so could someone ...
3 votes
1 answer
367 views
Write full box to topology file + script representation
I would like topo writelammpsdata to print the full box, while it seems only to be printing one molecule. I have loaded several molecules in a box with VMD - here ...
- 749
4 votes
1 answer
3k views
VMD Periodic boundary wrapping using pbc wrap
I am doing a simulation of multiple polymers which are named with segnames U(integer). During the course of simulation two polymers U5 and U10 interact with each other. However, because of periodic ...
- 453
4 votes
1 answer
190 views
How to study the stability of structure in water and analyze the radial distribution function (RDF)?
Context: If I have a system that consists of 20 structures. During molecular dynamics, these structures can form micelles from my point of view. I would like to do the following: Confirm if the ...
- 1,899
6 votes
1 answer
2k views
Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition
While calculating various quantities that involves particle positions ( for example, radial distribution function, mean square displacement etc.) using Molecular Dynamics simulation, the effects of ...
- 183
3 votes
0 answers
256 views
Formatting of text in label of VMD [closed]
I want to change the text formatting in the label's properties in VMD, as I want to use 1-based indexing rather than 0-based indexing. For now, %i in Format gives index on the screen, but I want to ...
- 1,456
4 votes
1 answer
1k views
Merging multiple PDB files in VMD using Tcl scripts?
I am trying to generate a matrix of small molecules arranged at locations (x, y, z) on a cube. I already have a Tcl script that can generate the required PDB and PSF files. However, I was wondering if ...
- 5,316
6 votes
1 answer
236 views
Time evolution of angle made by the helix with the normal to the plane using gromacs
I am new to the md simulation community. I have a peptide which is helical in a bilayer. I want to calculate the angle of the peptide relative to the bilayer with gromacs. For that, I created an index ...
- 63
4 votes
0 answers
74 views
Using LAMMPS and VMD to analyze a new structure [closed]
I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape ...
- 41