[gmx-users] NM analysis

Bert de Groot bgroot at gwdg.de
Wed Mar 27 16:30:08 CET 2002

Oleg Katchanov wrote:

> I have some problems with a Normal Mode analysis. 
> 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;

it's better to take cg for the later stages of minimization. Remember that
for NM, you need to have a fully minimised system (ie a maximal force
smaller than approx 0.01), steep is not efficient after the first 100 steps
or so. 

> 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

better use grompp -t traj.trr, to ensure you start with your minimised
coordinates in full precision. The last time I used NM, double precision
was required, but maybe this is not necessary anymore, maybe Berk or anyone else
knows this?

> 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?

this is not necessarily a problem. Actually, nmrun (or now mdrun, as the two were
merged, nm is just another integrator now in mdrun) does not do any integration 
steps, so you'll get nonsense averages and fluctuations. A better check would
be to scan the standard output of nmrun and g_nmeig, and look at the eigenvalues
critically (ie you shouldn't have any negative ones etc).


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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