[gmx-users] normal mode analysis and system size ...

Michael Brunsteiner mbx0009 at yahoo.com
Mon May 18 10:36:00 CEST 2015

hi ,
I've been trying to perform a nromal mode analysis using (after a thorough energy minimization of my system)

prompt> mdrun_d -v -s nm.tpr  -o nm.trr -mtx nm.mtx[...]
Maximum force: 8.56366e+00
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.Finished step 9060 out of 9060
Writing Hessian...

i ignored the warning hoping to get a away with that ... then:
prompt> gmx nmeig -f nm.mtx -s nm.tpr -v nmeig.trr
Reading double precision matrix generated by Gromacs VERSION 5.0.4
Full matrix storage format, nrow=27180, ncols=27180
Diagonalizing to find vectors 1 through 50...

and at this point it has been working for something like three days now and still going ...my system (a sample of a small organic molecule glass)  has about 10000 atoms(including protons) ... can anybody give me an estimate of what kind of system sizeis feasible for this kind of calculation? or could it be that gmx nmeig gets stuck (withoutwarning) when it encounters negative eigenvalues?


===============================Why be happy when you could be normal?

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