[gmx-users] normal mode analysis

[Bert de Groot]

Nguyen Hoang Phuong wrote:
> 
> Dear All,
> 
> I would like to perform the NMA for my peptide using GROMACS. First, the
> energy minimization is performed by using the conjugate gradient method
> and I got the maximum force:  5.87485e-02. Second, the program nmrun is
> run and the maximum force is 4.21849e+02. I got the negative values
> of the frequencies after the diagonalization of the Hessian.
> 
> My question is that why the later maximum force is much higher than the
> first one? Thanks for any explaination.
> 

are you sure that you take the lowest-energy conformation (in full precision)
for nmrun? you can extract it from the em trr file with grompp -t
 

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
____________________________________________________________________________