Re: [AMBER] calculating force correlation in trajectory

From: Lod King <>
Date: Thu, 28 Jun 2018 11:47:14 -0700

I am analyzing how the force in residue ABC is propagated and affected by
the neighboring residues, the motion between residue ABC and
residue DEFG...

if force-force time correlation function seems usable, I want to try this

it is the command typed:
> force-force time correlation or other more specific commands?


On Thu, Jun 28, 2018 at 11:37 AM, David A Case <>

> 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
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Received on Thu Jun 28 2018 - 12:00:04 PDT
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