Re: [AMBER] Inquiry on CPPTRAJ

From: Daniel Roe <>
Date: Wed, 3 Nov 2021 09:28:36 -0400


On Wed, Nov 3, 2021 at 12:13 AM Razil Tahir <> wrote:
> 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?

Yes, just make sure to specify the 'image' keyword with the 'hbond' command.

> 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.

Use the 'density' command with an atom mask selecting the atoms you
want. Check the manual for full details on both the 'hbond' and
'density' commands. You can look at the tests for each command (in the
$CPPTRAJHOME/test or $AMBERHOME/AmberTools/src/cpptraj/test
subdirectories) for additional examples (Test_Hbond and Test_Density
respectively). Hope this helps,


> Thank you in advance! I really appreciate your response!!
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Received on Wed Nov 03 2021 - 06:30:02 PDT
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