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Questions tagged [vmd]

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Homepage of VMD is http://www.ks.uiuc.edu/Research/vmd/

Main developer is University of Illinois at Urbana-Champaign

52 questions
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Default Representation/Drawing method in VMD

In VMD I want to load every new file with the drawing method CPK. This doesn't seem not to be an option in the .vmdrc file for some technical reasons. How can I do this from the VMD command line (so that I can make a script)? Or is there some other…
Jonatan Öström
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Tcl error : wrong # args: should be "set varName ?newValue?"

I tried to run the following Tcl script and got the error: wrong # args: should be "set varName ?newValue?" What does this mean? Note: The script includes terms specific to VMD program, such as mol and resid. Please disregard them. #count water…
melona
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How to load .prmtop and .crd files from Amber using MDAnalysis?

I am trying to load a .crd file from Amber, but this fails because it's not in the format MDAnalysis expect (see error at the end): topology = 'top.prmtop' trajectory = 'amberOut.crd' u = MDAnalysis.Universe(topology, trajectory) I saw this thread…
0x90
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Command history in Vmd text mode

How can I activate command history or autocomplete in VMD text mode (vmd shell) vmd > I use it in Linux Ubuntu, when I use arrow keys it prints characters like ^[[A.
Ahmad
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VMD/NAMD rmsd_residue_over_time returns no atoms selected

Whenever I run the rmsd_residue_over_time function from the residue_rmsd.tcl script from UI VMD/NAMD tutorial, it returns the error "no atoms selected". Specifically, I input the following, after loading my psf file and 20000 frames of my dcd…
C.A.B.
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Load multiple frames into psf file in VMD

How can I open a psf file in vmd and then load for this psf file multiple frames (dcd files) using line commands only ? I have like hundreds of dcd files and I don't want to do this manually.
dada
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Cannot concatenate dcd files in VMD using catdcd tool

I have a set of dcd files that I want to concatenante to have one (long) dcd file. I put in a VMD Tkconsole (VMD version : 1.9.2) the following code : catdcd -o output.dcd -i indexFile.ind input1.dcd input2.dcd input3.dcd and I had the following…
dada
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Using perl to run vmd tk console

Hey all for a program I am working on it uses pdb (protein data bank) files and computes the distance between all atoms from one another. I have a code that does this, however my personal and work computers don't have enough computing power to fully…
Heather Lynn
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Confused with psfgen module of VMD

I am fairly new to VMD and programming in general. I need to combine two pdb files of subunits into a combined pdb and psf file with both subunits. I used the Namd tutorial and used two pdb files named BChain270VerCTrue.pdb and barn_noH2o_ChainD.pdb…
ChrisG
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Tcl Unmatched open quote in list. VMD MMPBSA error

I've been trying to run MMPBSA calculations using CAFE, however, when I use -pb_rad charmm. VMD prints the following error when it begins to run PB calculations: "Unmatched open quote in list " I suspect that the error originates from the following…
Javier Wong
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Use proc from inside another proc on TCL

I'm trying to write a script in tcl to execute some analysis on VMD. First I'm creating an atom selection inside a procedure, then I'm trying to use it on another procedure. The atom selection from VMD is implemented as a Tcl function. The data…
Arthur Pereira
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How can I draw more than one pbc boxes on VMD?

Right now, I have: pbc box -color black -width 1 pbc set {4.541 4.541 6.463 69.5 69.5 90} How can I make another?
Prakriti Kayastha
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How to make 2 Fortran subroutines have the same output file?

I need the code to write the data of two circles in order to export it as an animation (vmd). This should give me around 6000 data(3000 per circle). When I run the program it only writes the data of the first circle. How do I write the two sets of…
Angel Uriel
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How can I merge 2 dcd trajectory files?

So I am in a situation where my 2 chains (2 proteins) from the same simulation are separately in 2 DCD files each having 2000 frames. I wanted to merge these 2 DCD files into single DCD file (which will have total 2000 frames) containing both…
dexterdev
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vmd does not open with filename in the command line argument in Mac OS X

I have recently shifted from Linux to Mac OS. I have installed vmd in this new machine. The vmd just load without any molecule when I type the following: vmd protein.gro This *.gro file contains a protein molecule. I want to open this file like in…
PythonNoob
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