Hi Chung-ke, Welcome to the relax mailing lists! Thanks to the hard work of one of the relax developers - Troels Linnet - this long calculation time should now be much, much shorter. Have a look at the following release announcement:
http://wiki.nmr-relax.com/Relax_3.3.0 For the 'CR72 full' model (http://wiki.nmr-relax.com/CR72_full), the clustering example here gives a ~22x speed up so your calculation time would then drop from ~20,000 min to ~1000 min. If you would like to receive announcements about new relax versions, please subscribe to the relax-announce mailing list (https://mail.gna.org/listinfo/relax-announce/). This list only receives ~10 emails per year. See http://news.gmane.org/gmane.science.nmr.relax.announce. I have a few questions about how you performed the analysis. Did you use a non-clustered set of results to seed the clustered analysis? In the dispersion auto-analysis protocol exposed via the GUI, the results from the non-clustered analysis will be taken as the starting point for optimisation of the clustered analysis, as described in Morin et al., 2014 (http://dx.doi.org/10.1093/bioinformatics/btu166). If you wish, and are capable with scripting, you can also create your own analysis protocol via a relax script and not use the auto-analysis. The relax software is very flexible and you can create quite complex analysis protocols - the auto-analyses are just large relax scripts. Also, did you look at the results from the non-clustered analysis to see if the kinetics of all 13 residues are similar? Or if the dispersion curves look reasonable? Some data might be of low quality and causing difficulties with the optimisation. You should also note that most dispersion data is not good enough to differentiate R20A from R20B. Do the final results (non-clustered and clustered) look reasonable for these two parameters? It could be that differentiating R20A from R20B in your system is difficult and causing optimisation to take much longer than normal. Do you see the same optimisation times with the clustered CR72 model where R20A=R20B=R20 (http://wiki.nmr-relax.com/CR72)? Also, have a look at the log file from the analysis and see if the total number of minimisation iterations is much longer for the 'CR72 full' model compared to the CR72 model. This will tell you if the optimisation problem is much more complicated for the 'full' model. Regards, Edward On 9 September 2014 09:19, Chung-ke Chang <chun...@ibms.sinica.edu.tw> wrote: > Dear all, > > This is my first post here, and I have a question regarding the time it takes > for a relaxation dispersion clustering process to finish. I have one > clustering calculation that has been running for ~ 20,000 min on a single > Xeon 2.66 GHz core. The cluster consists of 13 residues being fit to the > ‘CR72 full’ model. I wonder if the long time it is taking is normal? Would it > be possible that relax has been stuck in an infinite loop of some sort, > without showing up in the log file? Any input would be greatly appreciated. > By the way, using a cluster of only 11 residues out of the 13 did finish in > ~13,000 min. > > Chung-ke Chang > Biomacromolecular NMR Lab > Institute of Biomedical Science > Academia Sinica, Taiwan > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-users mailing list > relax-users@gna.org > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
