AMBER Archive (2005)

Subject: AMBER: Question about "nmanal"

From: Yen-Ting Lai (c54881028_at_mail.bio.ncku.edu.tw)
Date: Mon Jul 11 2005 - 09:11:25 CDT

Hello Amber users,

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?)

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")

Thanks in advance!
Yen

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