AW: vmd-l: moving atoms and updating distances

From: Norman Geist (
Date: Mon Feb 15 2016 - 00:11:47 CST



man, you don’t need that fixed stuff, just access the atoms properties directly using atomselect.




Set a [atomselect top “index 1000”]

$a set x 10.4


And don’t forget to use $a delete when using many atomselects within loops, to not produce a memory leak.


Norman Geist


Von: [] Im Auftrag von jing liang
Gesendet: Samstag, 13. Februar 2016 18:16
Betreff: vmd-l: moving atoms and updating distances




I need to introduce one atom in an existing molecule. I load the molecule

and then I load the "guess" coordinates of the extra atom. Then, I check out

the F (fixed) option in VMD for the molecule and only the extra atom is able to move.

After that, I try to compute the distance between the

extra atom and some existing atoms to improve the guess coordinates.


However, it seems that the distances are not updated in VMD using

this procedure. Is there a way to do this manual docking procedure in VMD?



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