AMBER Archive (2002)

Subject: Re: Nmode

From: James Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Thu Dec 19 2002 - 15:17:31 CST

Are you refering to doing NMODE on a periodic
box system? I don't think it's setup to do
that.

jim

On Thu, 19 Dec 2002, Pratul Agarwal wrote:

> Is it possible to do normal mode analysis (using
> nmode) on a system with explicit solvent in it? My
> system has about 150 amino acid residues and
> 6000 TIP3P water molecules. When I try to
> run nmode on this system (after resizing all relevant
> parameters), the program stops abruptly without
> giving an error message (but it dumps a core).
>
> Also, is anybody aware of a reference which describes
> the method used by nmanal to project the cartesian
> normal mode eigenvectors onto internal coordinates?
>
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