# [gmx-users] Normal mode analysis of pure water

simon sangma simoniitchem at gmail.com
Tue Oct 20 15:03:43 CEST 2009

```Hi,
I encountered the following remarks during normal mode analysis of pure
water. Can someone please suggest a solution.
mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log
-mtx nm.mtx
Reading file water.tpr, VERSION 4.0.4 (double precision)

Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...

starting normal mode calculation 'Pure Water'
648 steps.

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.
Finished step 648 out of 648

Writing Hessian...

gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg)

g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v
eigenvec.trr

Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading file water.tpr, VERSION 4.0.4 (double precision)
Reading double precision matrix generated by Gromacs VERSION 4.0.4
Full matrix storage format, nrow=1944, ncols=1944

Diagonalizing to find vectors 1 through 50...

One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...
Writing eigenfrequencies - negative eigenvalues will be set to zero.

Writing average structure & eigenvectors 1--50 to eigenvec.trr

gcq#132: "Shit Happens" (Pulp Fiction)

The eigenfreq is 0 which is the problem

The .mdp file used was;
;       User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
cpp                 =
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  nm
nsteps              =  10000
;
;       Energy minimizing stuff
;
emtol               =  0.01
emstep              =  0.01
coulombtype         =  PME
nstcomm             =  1
ns_type             =  grid
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091020/16efd3ca/attachment.html>
```