VMD terminates simulation before completion
I am trying to run a 1 ns simulation using VMD/NAMD on top of my 200 ps simulation, so I set the program to run 800000 with a timestep of 1. However, the next day (it took about 12 hours) it was...
View ArticleCommand 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.
View Articlehow to get an accurate number of frames in tcl script?
I have a trajectory contains 75 frames (*.dcd file). But when I try to calculate the number of frames by the tcl commands:set id [molinfo top get id ]puts [molinfo $id get numframes]I get much lower...
View ArticleHow 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...
View ArticleVMD/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...
View Articlevmd 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.groThis *.gro file contains a...
View ArticleHow can I draw more than one pbc boxes on VMD?
Right now, I have:pbc box -color black -width 1pbc set {4.541 4.541 6.463 69.5 69.5 90}How can I make another?
View ArticleHow 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...
View ArticleHow do I set representations properly in .vmdrc for VMD
I'm trying to setup default representations on load, and currently have added the following to the default .vmdrc file.display depthcue offcolor Display Background whitedisplay projection...
View ArticleDifference tcl script tkconsole to load gro file in VMD
My problem is simple: I'm trying to write a tcl script to use $grofile instead writing every time I need this file name.So, what I did in TkConsole was:% set grofile "file.gro"% mol load gro...
View ArticleInstalling VMD with python support on MAC
I have been trying to install VMD1.9.2 on a Macbook with python support but have not been able to. It seems to me that the packaged .dmg file for VMD comes without Python support. I have used the...
View ArticleTCL script to go through all folders in a directory and perform a function
File structureFile1 test.pdb xyz.txtFile2 test.pdb xyz.txtFile3 test.pdb xyz.txtI want to loop in through all folders in the directory and run the following code which is in textfile autopsf.tcl on Tk...
View ArticleHow to pass integers to tcl procedure in vmd
I am new in tcl programming and I need to write a script for vmd that calculates two distances between two couples of atoms and print them in an output file. I do not understand why measure can not...
View Articletrying to find out permeation events in each pore of AQP protein embedded in...
My project is based on MD simulation analysis on a system containing water box and lipid bilayer containing Aquaporin embedded in it. Simulations of timestep 150 ns is performed on this system to study...
View ArticleFile is not shown in the folder generated via tcl script
I am trying to write a file using tcl scripting (Via VMD). when I type command "dir" on tk/tcl console, it shows file name which I am trying to generate. But when I tried to open that file manually in...
View ArticleUse 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...
View Articlefinding difference between list elements in Tcl
I am a beginner in using Tcl. I am using it as VMD (molecular visualization) software uses it as a scripting language.I have a list of co-ordinates of atom positions for a protein like: {{1 2 3} {7 9...
View ArticleControlling external program with python
for my studies I need to process a lot of data. The data needs to be analyzed by a program called VMD and should finally be stored in an excel sheet. My aim is to automate the whole process instead of...
View ArticleHow to calculate the average of each column with Tcl script
I need to calculate the average of each column with a tcl script from a text file please help meFrame Time Elec VdW Nonbond Total0 0 -216.63 -16.0174 -232.647 -232.647 1 1 -196.786 -28.6093 -225.395...
View ArticleTK/TCL console does not run full script, but works with manual input
New programmer here. I have been trying to run my script through Tk console through a VMD program which works when I copy it into tkconsole, however when I source/load my script into tkconsole, it only...
View ArticleTcl 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...
View ArticleHow do I auto generate multiple VMD representations from a list of ids in tcl...
I am new to tcl. I have the basics down but I hope to get better. I have a list of lists of ids that I want to select from a molecule for visualization. I want to apply different coloring to each rep...
View ArticleTcl print cwd and use it as string
I was making a small script in tcl for VMD:mol load psf run_1/structure.psf xtc run_1/postDocking_wrapped.xtcset final [atomselect top "not (water or ions or resid 1216)" frame last]$final writepdb...
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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...
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Tcl foreach loop not finding second variable
I am sure this has been asked here before but I can't seem to find any link that can help me with my particular problem.I am using tcl scripting within vmd to do a quick analysis.package require...
View ArticleWriting Python or TCL VMD scripts [closed]
Does anyone know a complete tutorial to learn about writing Python or TCL scripts?I want to write a script to load a molecule , make 3 representations of it,and change attributes(like coloring method,...
View ArticleTCL (VMD scripts) functions in python
I have access to a bunch of TCL scripts but some of them are not working fast and I want to convert some of them to python. Does anybody have any experience? ex. one of the functions that I faced...
View ArticleImportError When Attempting to Use VMD After Installation
I recently attempted to use the Variational Mode Decomposition (VMD) package in Python. After successfully installing the package with the command pip install vmd, I tried to import it into my project...
View ArticleAbout making animation by VMD(Visual Molecular Dynamics)
~Details~I have a file.pdb that contains 10 frames but each frame don’t have same data size(ex. frame1 has 10 atoms, frame2 has 20 atoms….).I need a way to make animation of this file, but VMD...
View ArticleDefault 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...
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