VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed May 13 2015 - 13:44:50 CDT

Also, you need to make sure your for loop is doing this sanely. Here is
how I'd approach it:

set a [atomselect top "index < 1338 and name Si and y>9 and within 5 of atom O]
set t [atomselect top all]

for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {

$a frame $i ; #changes the frame the selection will be based on
$a update ; #Rechecks that its selecting the right stuff
$a set name C
$a set type C
$a set element C

}

However name, type, and element are not per-frame fields, so you do know
that you'll be changing it for all of them, right?
-Josh

On 05/13/2015 01:07 PM, Maxim Belkin wrote:
> Hi,
>
> Have you tried the following?
>
> animate write xyz output.xyz beg 0 end -1 waitfor all
>
> Maxim
>
>
>> On May 13, 2015, at 12:53 PM, JeJoon Yeon <sonicturbulent_at_gmail.com> wrote:
>>
>> 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,
>