[gmx-users] Essential Dynamics Sampling (EDS) MD

Bert de Groot bgroot at gwdg.de
Fri Jan 12 14:49:09 CET 2007

Ran Friedman wrote:
> Dear Bert,
>>The Jacobi error hints at a fitting problem. If not the starting
>>position, could it
>>be the target that's causing the problems?
>>Please check the head of the .edo and log files, to see if the
>>reported RMSD's
>>are what you would expect and especially if reported projections are
>>compatible with
> Do you refer to EDx? The values are not equal to what I get from g_anaeig.

then there's possibly some mixup between fitting reference and/or selection
and/or the eigenvectors between g_anaeig and make_edi?

Please make sure that group selections and reference groups (-s option
of make_edi, g_covar and g_anaeig) are identical. Check covar.log if you're
not sure anymore which fitting structure/selection you chose for g_covar.

If you still have problems, please feel free to contact me off-list with a minimal
set of files with which the problem can be reproduced.



Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

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