Difference between revisions of "Tricks in VMD"
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display projection Orthographic; # Orthographic/Perspective | display projection Orthographic; # Orthographic/Perspective | ||
Note that the directory, with unknown reason, might be encrypted so you have to open it by typing <code> vi vmd.rc </code> in the Tk console. | Note that the directory, with unknown reason, might be encrypted so you have to open it by typing <code> vi vmd.rc </code> 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 | ||
Latest revision as of 17:17, 9 December 2014
Contents
[hide]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
