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

Bert de Groot bgroot at gwdg.de
Thu May 15 12:43:01 CEST 2003

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).



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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