AMBER Archive (2004)

Subject: AMBER: nmode analysis

From: sebnem (sebnem_at_mercury.chem.pitt.edu)
Date: Sun May 02 2004 - 19:52:12 CDT

Hi, I am using nmode analysis module in amber7 to find the normal mode
frequencies of a small peptide. The frequencies are ok, but some of the
corresponding eigenvectors of very low frequency modes have all zero
eigenvectors. According to the eigenvectors of these very low frequency
normal modes , only one atom out of 84 is moving. Acoording to common
sense these low frequencies should correspond to collective motion. I
wonder whether there is a bug in this part.
P.S: I am nearly using the same input file which you have in
amber7/tutorial/crown_ether/nmode/nmode.in except a different atom number.
thanks in advance

Sebnem Essiz

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