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

[Bert de Groot]

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
>>g_anaeig.
> 
> 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.

cheers,

Bert

______________________________________
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
http://www.mpibpc.mpg.de/groups/de_groot