Tricks in VMD

Use the text-mode VMD just like bash!

//Currently it is only applied to VMD in Linux

Google rlwrap which is a readline wrapper, a small utility that uses the GNU readline library to allow the editing of keyboard input for any other command. It maintains a separate input history for each command, and can TAB-expand words using all previously seen words and/or a user-specified file. Install the program and type

rlwrap vmd -dispdev text

How to make default background color to white

Add the following lines to vmd.rc under the program directory of VMD

# color
color Display Background 8
color Display FPS 16
color Axes Labels 16

# display
display projection Orthographic; # Orthographic/Perspective

Note that the directory, with unknown reason, might be encrypted so you have to open it by typing vi vmd.rc in the Tk console.

Useful notes from the mailing list

27 Nov 2014

A few points. DCD files store coordinates in single precision only, not double precision. Restart files are often double precision, but most trajectory formats are only single precision. The various "measure" routines in VMD are dominated by single precision since that's how VMD also stores atomic coordinates associated with trajectory frames currently. Tcl math routines are mostly double precision, so there will be differences in rounding, vector length normalization, etc if you invoke routines that are doing math in the more conventional Tcl way. In any case, since your atomic coordinates in VMD are currently only stored in single precision, that's all you should expect from most distance measurements and the like. Since floating point is non-associative, any change in the order of operations (even a tiny one) can cause the results of two otherwise comparable calculations to differ, so your results are exactly what I would expect to see.

-- J. Stone