So, are you trying to modify the laws of Physics to prevent the simulation
from providing physically accurate results?
James Kress Ph.D., President
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-----Original Message-----
From: 李脈玉 <santaclaus.sjtu.edu.cn>
Sent: Friday, April 23, 2021 10:19 AM
To: amber <amber.ambermd.org>
Subject: [AMBER] Make the two ligands independent in one simulation
Hi, Amber users
Thanks for your attention!
I would like to study two ligands binding behavior in one protein system
simultaneously in a single MD trajectory.
However, the ligands prefer to aggregate together due to the polarity.
I am wondering is there any possible way to make those two ligands
independent in a single MD trajectory.
In other words, there is no non-bond energy between the two ligands, so that
they can move independently though they are in one protein system!
Many thanks
Pineapple
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Received on Fri Apr 23 2021 - 12:30:02 PDT
