Re: [AMBER] calculating force correlation in trajectory

From: Lod King <>
Date: Thu, 28 Jun 2018 16:30:06 -0700

I have found any papers mentioning force analysis in MD analysis about a
but because MD model is based on Newton's 2nd law where F=ma=m (dv/dt), and
our trajectory has velocity for each atom, I do believe F can be one of the
factors, just like coordinates that can be analyzed, I just have done any
with AMBER CPPTRAJ yet..

My colleague is trying to convert trajectory into GROMACS format where it
can extract force from that ( maybe).

yeah, if anyone knows it, please post reply here, I really appreciate it..

On Thu, Jun 28, 2018 at 3:04 PM, David A Case <>

> On Thu, Jun 28, 2018, Lod King wrote:
> > 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...
> Probably the best thing to do is to find a published paper that reports
> the sort of analysis you would like to do (or something close to it).
> Then look at the methods section to see how it was done.
> I'm doubtful that analyzing forces will do you much good. Looking for
> "the motion between residue ABC and residue DEFG" sounds like something
> that involves analysis of coordinates, not forces.
> But maybe someone on the list knows of analysis that sounds like what
> you describe above.
> ....dac
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Received on Thu Jun 28 2018 - 17:00:02 PDT
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