[gmx-users] eigenvalue~

[Bert de Groot]

F JH wrote:
> 
> Hi~
> 
> I used CHARMm normal mode analysis for my target protein and got a
> reasanable result.(The first six frequencies is nearly zero).
> 
> Now I use GROMACS and run a normal mode analysis.When I use g_nmeig to
> calculate my new eigenvalues,I found eigenvalue is strange.It
> contains positive and negative values and the final value is much lager
> than CHARMm normal modes analysis.All above was not found in my CHARMm
> results.
> 
> It's my mdp file
> 
> title                    = 0108
> cpp                      = /lib/cpp
> include                  = -I../top
> define                   =
> integrator               = nm
> 
> How should I improve my job?
> 

-you should properly minimise your structure before doing nm (cg and not steep)
-you should use grompp -t to extract the last frame from your EM.trr file
 (otherwise you loose precision if you take confout.gro)
-you may have to use the double precision version of gromacs.

--

Bert

ATTENTION: Please note new phone/fax numbers below!

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________