[gmx-users] Normal mode analysis of pure water

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 15:09:06 CEST 2009

simon sangma wrote:
> Hi,
>     I encountered the following remarks during normal mode analysis of 
> pure water. Can someone please suggest a solution.

You've been told twice already what the likely solution is:


> Maximum force: 2.74758e+03
> Maximum force probably not small enough to ensure that you are in an
> energy well. Be aware that negative eigenvalues may occur when the
> resulting matrix is diagonalized.


> One of the lowest 6 eigenvalues has a non-zero value.
> This could mean that the reference structure was not
> properly energy minimized.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list