Hi all,
I am having some troubles with the following problem:
I have a trajectory stored in a file having XYZ format - let's assume it
has 10 states in total.
At the very beginning I have 5 atoms connected in a loop (like in
cyclopentane):
ATOM1 - ATOM2
ATOM2 - ATOM3
...
ATOM5 - ATOM1
I create bonds by:
"bond ATOM1, ATOM2"
and so on.
However in my simulations at some point (let's say in state #4) a new
element is introduced.
If that happens I must break a bond ("unbond" command) between e.g. "ATOM1
- ATOM5" and then then create two new bonds:
"ATOM1-ATOM6"
and
"ATOM5-ATOM6"
So what I want to obtain is a bond between atoms 1 and 5 up to the state
#4, at the time of #4 I want to break a bond and create two new ones, and
from that moment proceed with the new bonds' topology - so I can render
every frame with a correct bonds network.
Moreover my trajectory files are usually too large to use "split_states".
Any ideas how to work this problem out?
Thanks,
Pawel
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