Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory

From: David A Case <>
Date: Sun, 24 Jun 2018 16:18:15 -0400

On Sun, Jun 24, 2018, Lod King wrote:
> I would like to extract the force for each atom in a 100ns run trajectory.
> I have a folder containing:
> prmtop file
> dcd file (combined from 10 mdcrd files, each 10ns)
> 10 mdcrd files

Do these files contain forces, or coordinates? That is, how did you
create the mdcrd files? If you didn't set the "ntwf" parameter, your
mdcrd files will just contain coordinates, and you cannot extract forces
from these.

If you did use ntwf, then you have the forces for each atom, at each
time step that was saved. You can load this as a "dataset" into
cpptraj, and use its commands to perform various types of analysis, such
as averages, time-correlation functions, etc. If you need some other
type of analysis, you will need to write your own scripts to analyze the
data: pytraj can help a lot if you are comfortable using that language.

...hope this helps....dac

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Received on Sun Jun 24 2018 - 13:30:03 PDT
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