Re: [AMBER] calculating force correlation in trajectory

From: David A Case <>
Date: Thu, 28 Jun 2018 14:37:13 -0400

On Thu, Jun 28, 2018, Lod King wrote:
> I would like to analyze the force correlation between residues in a 200ns
> trajectory
> my input file contains ntwf = -1 as suggested.

It's not clear what you mean by "force correlation": do you want to know
how the forces on atom A correlate to those on atom B? Or do you want a
force-force time correlation function? Or something else?

Force analyses are not all that commonly done by current Amber users, so
you may need to write a specialized script. On the other hand, Dan has
written cpptraj to be remarkably flexible, so don't give up on it. But
you'll need to come up with an exact mathematical description of what
you want.

Also, don't underestimate the value of just browsing through the cpptraj
chapter in the manual to find something that is close to what you want
to do.

....good luck....dac

AMBER mailing list
Received on Thu Jun 28 2018 - 12:00:03 PDT
Custom Search