Re: [AMBER] info on trajectory files

From: Dr. Anselm Horn <>
Date: Wed, 19 Dec 2018 11:12:01 +0100

> How to do trajectory fitting, i.e. Global Rotation and global translation,
> on the trajectory files(.nc) generated from production phase of MD
> simulation of a protein system?

Simply use cpptraj to perform a rmsd fit (e.g. for all atoms in all
residues or only on the CA atoms) for your trajectory.

Please see the Amber18 manual, section "cpptraj", command "rmsd". There
are several examples (Search for "rmsd").
The actual command is explained on p. 676-678.



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Received on Wed Dec 19 2018 - 02:30:03 PST
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