[gmx-users] NM analysis

[Oleg Katchanov]

    Dear GROMACS users & autors!

I have some problems with a Normal Mode analysis. If I understood it 
right, for this analysis I need only the energy-minimised conformation 
of my protein in vacuum.
(In the case prot. in water the program nmrun abuse me with the text
"No option -table
starting nmrun "In water" and begins to calculate the gigant matrix ...)

I have done the following operation:

editconf -f MOL.gro -o MOL.gro
grompp -f em.mdp -c MOL.gro -p MOL.top -o MOL_em.tpr
#integrator steep in em.mdp;
mdrun -nice 4 -table table6-12 -s MOL_em.tpr -o MOL_em.trr -c 
MOL_after_em.gro

grompp -f md.mdp -c MOL_after_em.gro -p MOL.top -o MOL_nm.tpr
#integrator md in md.mdp;
nmrun -s MOL_nm.tpr -m MOL_hess.mtx
g_nmeig -f MOL_hess.mtx -s MOL_nm.tpr -o MOL_eigval.xvg -v MOL_eigvec.trr

After this g_nmens, g_anaeig analyses the eigenvectors. As output I get 
the empty box (ensemble.xtc, filtered.xtc, etc.)
How I understood, I'm doing something wrong with the nmrun, because in 
the file nm.log after the creating the hessian matrix all of the average 
values and RMS values are zero:

        <======  ###############  ==>
        <====  A V E R A G E S  ====>
        <==  ###############  ======>

   Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00
   Total Energy    Temperature Pressure (bar)
    0.00000e+00    0.00000e+00    0.00000e+00

etc.
Why is it so? May be, I have to change something in the md.mdp file? 
What the integrator must be used for nmrun?
Sorry, when any question are... mmmm... stupid. :-( I'm just the 
beginner in this things.
Thank you in advance!

Oleg Katchanov.