Hello Chris, thanks for the reply. Below his message commented walkthrough.
In your email you asked me for quantitative results. All I have so far is
a visual inspection of the pulling trajectory. All I can see are
the two molecules moving linearly away from each other in a rectangular box
of dimen
Dear Chris, I'm so sorry for surperficial email.
You are correct because in the previous message
I forgot to mention that now the simulation was
performed in water (naturally with PBC).
The main parameters of the simulation are given below.
As I said, I wish to keep the displacement of the pulled m
Hello Chris, thanks for the tips, they were very helpful.
Now a new problem appeared. I'm trying to separate the
two benzene molecules from one another while maintaining
the displacement vector aligned with the z axis. For that I
have used "pull_geometry = direction". However, at the end of the
sim
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