Dear Amber users,
I am trying to run a steered MD simulation to study protein unbinding
mechanisms. Now, I can see that my simulation is crashing as the atom I
pull is leaving my periodic box and interacting with its image.
So, I wanted to define an asymmetric box such that I can have one of the
axes to be greater in dimension than the other two. Now, can this be done
in Amber? Whenever I have used solvateBox it always generates a somewhat
symmetric box. I tried to follow the crystal simulation where asymmetric
boxes can be but I was not so sure if that would be the correct way to do
and I could not follow it properly as well.
This seems like a very trivial problem and someone must have dealt with it
before. I would be very grateful if I could get some suggestions about it.
Thank you in advance.
Regards,
Souvik
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Received on Wed Apr 15 2020 - 16:00:02 PDT
