[gmx-users] non-symmetric matrix and too large first values
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:
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users