[AMBER] Inquiry on CPPTRAJ

From: Razil Tahir <raziltahir.hotmail.com>
Date: Wed, 3 Nov 2021 04:13:02 +0000

Hello experts!

I'm currently in the stage of analyzing lipid bilayer MD simulation using CPPTRAJ packages in Amber. I have a few questions.

Firstly, I'm using periodic boundary condition. So, can I study interaction between atoms in different cells? For example, the hydrogen bonds between the primary cell and its adjacent cells?

Secondly, I want to plot local density profile. Can I group a few atoms together? For example, I need one plot for the lipid head and another one for the tail? I looked in the tutorial but I can find it.

Thank you in advance! I really appreciate your response!!
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Received on Tue Nov 02 2021 - 21:30:02 PDT
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