[gmx-users] Normal mode analysis of pure water

Berk Hess gmx3 at hotmail.com
Tue Oct 20 15:44:18 CEST 2009

This is wasting a large amount of CPU time.
Water is solid (ice) at 0 K.
A plain normal mode analysis would give you the normal modes of ice.
You can do a normal mode analysis of liquid water without minimization,
but the standard NMA techniques will not work.


Date: Tue, 20 Oct 2009 18:33:43 +0530
From: simoniitchem at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Normal mode analysis of pure water

    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
Getting Loaded...

Reading file water.tpr, VERSION 4.0.4 (double precision)
Loaded with Money

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

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