[gmx-users] Normal modes

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 8 20:18:45 CEST 2001

On Mon, 8 Oct 2001, Andrew Horsfield wrote:

>Step 9, E-Pot = 3.2854699832e-19, F-max =  2.14438e-07
>This is clearly well converged. Then I build the hessian, and finally I
>diagonalise it. The program for building the Hessian (nmrun_d) complains
>  Maximum force: 8.59693e+01
>  Maximum force probably not small enough to ensure that you are in a 
>  energy well. Be aware that negative eigenvalues may occur when the
>  resulting matrix is diagonalized.
Are you using the confout.gro file from mdrun? That has limited accuracy
and hence may lead to this. You can write out a confout.g96 instead:
mdrun -c confout.g96

Don't know about units. Isn't it in the manual?

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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