Questions tagged [vmd]
Questions about the Visual Molecular Dynamics (VMD) structure visualization program.
39 questions
5
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1
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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 ...
4
votes
0
answers
66
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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
482
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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
295
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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
302
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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 ...
- 699
4
votes
1
answer
2k
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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 ...
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4
votes
1
answer
147
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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 ...
- 1,652
6
votes
1
answer
1k
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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 ...
- 163
3
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0
answers
192
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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 ...
- 1,416
4
votes
1
answer
917
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 ...
- 4,066
6
votes
1
answer
175
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
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0
answers
47
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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
3
votes
1
answer
55
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What package do I use to model a material and get the LAMMPS data file as an output?
VMD has a nanotube builder that I can use to build CNT and then using topotools I am able to produce the data file for LAMMPS. For my specific research I need to create a fake CNT with triangular ...
5
votes
1
answer
396
views
How to apply colors and graphics to VMD from Tcl?
I have a collection of pdb files (15), and I want to basically apply the same visualization settings on each one of them and render the image.
I want the above settings, with a certain, resolution ...
- 4,181
3
votes
0
answers
47
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which atom_style to be able to simulate a heating a CNT in water in edpd model? [closed]
I am trying to use energy conservative dissipative dynamic (edpd) model to simulate heating a flexible CNT which is floating inside a liquid (water). Using create_atoms command I am creating my liquid ...
2
votes
1
answer
98
views
Why is my pdb looking so weird? [closed]
I have generated the following pdb file for a polymer:
...
- 4,181
6
votes
2
answers
4k
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How to show orientation axis in Pymol
Is there a way to show the orientation axis in Pymol?
It's something like this in VMD. I much prefer Pymol rendering.
- 1,674
2
votes
1
answer
62
views
Flink installation question on MacOS Monterey?
I want to make a movie using VMD, but when I follow the instructions it can just produce the image frames in the ppm format. I noticed I need to preinstall some packages for VMD to be able to make a ...
4
votes
1
answer
315
views
Extracting bond information from the xyz positions of atoms?
I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD?
I want to create a LAMMPS input file that contains not only ...
8
votes
2
answers
326
views
Limits of periodic box from pdb
I have a pdb file of some solvent molecules in a box of 20 Angstroms I have built using Tinker. I have opened the file with Chimera, Molden, Pymol and Avogadro... but I would like to see, and maybe ...
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6
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1
answer
4k
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How do I use a LAMMPS initial data file in VMD to see the material structure?
I learned how to create an initial data file for LAMMPS using VMD, So I can get all the position and bonding information.
My question is:
I have a LAMMPS initial data file which only has the positions ...
3
votes
0
answers
57
views
Is it possible to build a carbon nanotube from a triangular lattice using Material Studio? [closed]
I was looking for a way or a software to construct a carbon nanotube from a triabgular lattice. I need to create triangular lattice CNT to use it in VMD (as VMD just has the regular hegzagonal CNT) ...
4
votes
0
answers
78
views
Is it possible to generate a non-predefined nanotube in VMD? [closed]
I know that generating a Carbon Nanotube (CNT) in VMD, I can get the required LAMMPS input file. Since VMD makes my life way easier, giving me the position, angle and bonding information in the format ...
5
votes
2
answers
304
views
How to generate CNT bond-type information for LAMMPS intial file?
I have just started working with VMD, and I figured out how to generate a Carbon Nano Tube (CNT) in VMD and save it's atom positions to use as initial file in LAMMPS. My question is, if you know of ...
6
votes
1
answer
3k
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How to add a bond between two atoms in VMD?
I want to add a bond between specific atoms.
I found on VMD page that one can use topotools (e.g. topo addbond 1 2 ), but I have a lot of residues so this method ...
- 1,652
8
votes
1
answer
312
views
How to assign "Trajectory Smoothing Window Size" inside VMD Tcl script
Currently in my VMD display, I define the Trajectory Smoothing Window Size
in the dialog box as below.
Figure below is for protein selection, the Trajectory ...
- 1,674
10
votes
2
answers
1k
views
Molecular dynamics frame distorted by VMD?
I am running a VMD renderer to view my GROMACS molecular dynamics output.
At one frame, the geometry looks fairly normal like this:
At another frame, it displays a distorted geometry, with the ...
- 1,674
6
votes
1
answer
2k
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How to visualize protein-ligand complex MD run using VMD
GROMACS version: gmx, version 2021.4
GROMACS modification: No
I'm following the Protein-Ligand Complex tutorial.
I'd like to visualize the binding using VMD.
I use the output from these commands:
<...
- 1,674
5
votes
1
answer
357
views
VMD polymer draws multiple bonds
I'm new to VMD and I'm having some problems with displaying my polymer chain. Instead of just one bond, VMD draws multiple bonds. Why does this happen?
I'm creating the data with Lammps, below you can ...
- 51
8
votes
0
answers
331
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How to add double bonds to hexagons when creating a graphene layer in VMD? [closed]
When creating a Graphene layer in VMD using the Nanotube Builder it only generates hexagons with single bonds because of this errors occur when creating the topology for gromacs software using,
...
- 367
6
votes
1
answer
5k
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How to show electrostatic interactions in Pymol or other on the wanted residue
I have the following Pymol visual,
The green molecule is receptor and red/yellow is the ligand.
In the ligand I highlighted Lysine (K) residue as yellow.
What I want to do is to highlight and draw ...
- 1,674
13
votes
1
answer
900
views
How to calculate RDFs for MD trajectories without PBC, directly from coordinates? [closed]
I have been running MD simulations on water droplets with an ion in them. I am trying to implement a program that could calculate the radial distribution function from ion to oxygen (or ion to ...
- 7,171
6
votes
1
answer
525
views
Can VMD change its cartoon representation for secondary structure according to trajectories?
I am using VMD to visualise the secondary structure of protein here.
The trajectories are from my Gromacs simulation. Firstly I use ...
- 171
6
votes
1
answer
1k
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Secondary structure information at each frame in a VMD trajectory
I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list
to calculate the secondary structure ...
- 453
8
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2
answers
2k
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How do I build and run a simulation of water molecules in NAMD?
So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
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8
votes
2
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540
views
File type to write bond information
I have an xyz file upon which after processing in Python, I determine bonds between different atoms. What would be the correct file type that I can write to visualize this bond information in VMD?
- 1,083
11
votes
2
answers
2k
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How to include individual PBC box dimensions in xyz file format compatible with VMD
I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this:
...
- 1,083
11
votes
2
answers
2k
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Recalculate atom positions to account for periodic boundary conditions
I have the output of a simulation done using Periodic boundary conditions (PBC), however, the atom positions have been resolved, i.e. there are atoms outside the PBC-box now. Is there a software/...
- 1,083
11
votes
1
answer
2k
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Calculating RMSF in VMD
As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...
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