[gmx-users] non-symmetric matrix and too large first values

[Bert de Groot]

medeawan at sohu.com wrote:
> 
> dear all,
> I want to calculate the Normal Mode of some proteins and DNA in vacuum. When I use the command g_nmeig_d after EM(Max force < 1e-7), for some structures everything is ok (the first six eigenvalue <1e-4), but for some structures I get the following message:
> "possible non-symmetric matrix:
> x[311][103]=2.017657e-04,x[103][311]=2.017515e-04
> .........
> 
> One of the first eigenvalues has a non-zero value.
> This could mean that the reference structure was not
> properly energy minimised"
> and for others only the "possible non-symmetric matrix" message.
> Is there something wrong?

hmm, did you check those eigenvalues? Are the non-zero ones *really* significantly
different from zero? 

(the thresholds for the warnings about non-symmetry and non-zero first 
eigenvalues were empirically determined from a number of test systems. 
It could be that for your combination of EM scheme and molecular system 
these thresholds are too strict).

--

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
____________________________________________________________________________