[AMBER] Tutorial B0

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Thu, 27 Aug 2020 07:52:38 +0000

Some suggestions regarding potential modifications to the tutorial which might be useful.

"From here, you can examine the topology, structure, atom names, atom types, and partial charges of the molecule. Basic editing of the molecule is also possible."
-->> If you are are on macOS using XQuartz, you will need a USB connected "PC" mouse and keyboard to enable all the functionalities in the GUI "edit" mode. The settings available to translate a trackpad and/or wireless mac mouse/keyboard is not working properly.

Given suggested input for CPPTRAJ on the website is:

    trajin 02_Heat.nc
    trajin 03_Prod.nc
    reference 01_Min.ncrst
    rms reference mass out 02_03.rms time 2.0 :2

However, the explanation is still referring to the two-step process:

    center :1-3 mass origin Center the residues 1-3 by mass to the system origin
    image origin center Image the atoms to the origin using the center of mass of the molecule

This should likely be replaced with

    autoimage Automatically center and image (by molecule) a trajectory with periodic boundaries, the atoms of the ’anchor’ region (default the entire first molecule) will be centered

So that the input and explanation are the same.

Everything seems to be working fine, nice tutorial.
Best regards
// Gustaf
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Received on Thu Aug 27 2020 - 01:00:02 PDT
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