[gmx-users] NM analysis

[Bert de Groot]

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).

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________