Re: [AMBER] Extract Force from MDCRD/DCD trj

From: David A Case <>
Date: Fri, 27 Jul 2018 08:21:12 -0400

On Thu, Jul 26, 2018, Lod King wrote:
> I used the following commands:
> >parm xxx.prmtop
> >trajin md01.mdcrd
> >trajout md01_1.out
> >go
> however, I obtained a very big output file (like 20GB, my mdcrd is also
> 20GB), with numbers which seems randomized, I dont see any "force to atom"
> patten specifically.

This is what I would (maybe naively) expect: forces on atoms are very
rapidly varying and will probably appear random. Have you looked at a
very small molecule (even with only 2 or 3 atoms) to make sure you
understand what you are looking at?

Remember that force on any given atom will change sign a couple of times
every vibrational period. One sort of analysis would compute the
force-force time correlation function (sampled at, say, 10 fs sampling
rate), then Fourier transform it to get a vibrational spectrum. So be
sure you know *exactly* what analysis you want to do.


AMBER mailing list
Received on Fri Jul 27 2018 - 05:30:02 PDT
Custom Search