[gmx-users] g_anaeig Error!

[Tsjerk Wassenaar]

Hi Yao,

The help says:

 -[no]m          (yes)

     Divide elements of Hessian by product of sqrt(mass) of involved atoms

     prior to diagonalization. This should be used for 'Normal Modes'
analysis

So for NMA you need to us -m (which is default). With -nom you do not
divide by the masses.

Cheers,

Tsjerk

On Fri, Apr 10, 2015 at 1:38 PM, xy21hb <xy21hb at 163.com> wrote:

> Dear all,
>
> I am trying to calculate entropy using g_anaeig (Gromacs version 5.0.1),
> after using g_nmeig to calculate eigenvectors and eigenvalues (after
> computing hessian matrix):
>
> g_nmeig_mpi -f hessian.mtx -s run.tpr -nom
>
> g_anaeig_mpi -v eigenvec.trr -entropy
>
> But I am getting the following error:
>
> Fatal error:
> Can not calculate entropies from mass-weighted eigenvalues, redo the
> analysis without mass-weighting.
> ----------------------------I would think -nom gives non-mass-weighted
> eigenvalues, but it seems not.Could someone help me with this?
>
> ------------------------------
>
> Thanks and Regards,
>
>
> Yao
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.