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

David spoel at xray.bmc.uu.se
Thu May 15 08:36:01 CEST 2003

On Thu, 2003-05-15 at 04:35, 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?

You say you run g_nmeig after EM. Have you run the normal mode analysis?
This is an option in mdrun (algorithm = nm)?

Otherwise, is this all in double precision?

> Thanks for any help.
>                                              Sincerely yours
>                                                     Medeawan
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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