Re: AMBER: Question about "nmanal"

From: David A. Case <>
Date: Mon, 11 Jul 2005 09:15:32 -0700

On Mon, Jul 11, 2005, Yen-Ting Lai wrote:
> I've performed a quasih analysis of my trajectory and I'd like to project
> the whole trajectory onto a specific mode. My questions are about the
> "nmanal" program:
> 1) In the Amber7 manual, it specifies the usage of nmanal as: "nmanal
> [-O] -i nmdin -o nmdout -p prmtop -v vecs -r rvecs". I didn't see any way
> to give a trajecctory file. Or shall I specify the trajectory file in the
> input file(nmdin)? Then what is the key word I should use? (I know I should
> use 'ntrun=8' to project trajectory snapshots onto normal mode directions,
> but where to give the trajectory file?)

Trajectories are read on stdin, that is, you would invoke something like this:

   nmanal -i nmdin -o nmdout -v vecs -m mass < trajectory-file

Note the "-m mass": you need to have a file (default name is "mass") whose
free-format contents contain the natom masses for your system.

Heaven knows, of course, if ntrun=8 in nmanal actually works. This was all
re-written for Amber 8 (see the "projection" command in ptraj).

> 2) Is the format of the normal mode vector files produced by quasih
> different from that of nmode output? Will I encounter problem if I give a
> vector file from quasih program?(because I have a feeling that "nmanal" is
> designed for "nmanal")

The format for quasiharmonic modes and for "real" normal modes is the same.

....good luck...dac

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Received on Mon Jul 11 2005 - 17:53:00 PDT
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