VMD-L Mailing List

From: JeJoon Yeon (sonicturbulent_at_gmail.com)
Date: Wed May 13 2015 - 12:53:27 CDT

Hello all

I can swap specific atoms for a single frame xyz only. Like

mol new test.xyz type xyz waitfor all
set a [atomselect top "index < 1338 and name Si and y>9 and within 5 of
atom O]
$a set name C
$a set type C
$a set element C
set t [atomselect top all]
$t writexyz swapped.xyz

But how can I do this with multiple frame? I tried to use for loop but
1) Sometimes it causes error
2) Sometimes it swaps the specific atoms for all frames, but the criteria
is based on only last frame's xyz position.

So I don't know what to do anymore. Can anyone help or modify that single
frame code to work for multiple frames? Is this coming from read / write
problem?

Thanks

Best,