Ok, Im sorry to insist but I am probably missing something here. How do I state which bound goes with which parameter? That is, which position in the array bound corresponds to the S2f parameter? Regards. TP
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 6 de Abril de 2011 17:42 To: Tiago Pais Cc: [email protected] Subject: Re: How to set S2f to 0.111? Hi, That is roughly correct. Just set the lower and upper bound to 0.111 and set the number of increments for that parameter to 1. Then it is like a grid search without S2f being present, or being fixed to 0.111. Regards, Edward On 6 April 2011 18:38, Tiago Pais <[email protected]> wrote: > Hi Ed, > Thanks for the quick reply. > Let's see if I understand your suggestion. For example, the mf_multimodel.py > sample script performs a grid search minimization using the grid_search > function. So if I insert an array of upper and lower bounds for the > parameters in the model I can constrain the interval of possible results, > correct? If so, what is the sequence for the parameters in the array? > TP > > > > -----Original Message----- > From: Edward d'Auvergne [mailto:[email protected]] > Sent: quarta-feira, 6 de Abril de 2011 17:13 > To: Tiago Pais > Cc: [email protected] > Subject: Re: How to set S2f to 0.111? > > Hi, > > Unfortunately, there is no ability to fix one of the model-free > parameters during optimisation in relax yet. This is something that > has been requested one or two times over the years. This is > complicated as the gradients and Hessians (first and second partial > derivates) need to be modified with this in mind, as the curvature of > the space changes. The fixed parameter is not part of the gradient or > Hessian, and has to be removed. This really complicates the target > function, gradient, and Hessian and, due to the low demand, has not > been implemented. > > Are you able to optimise this parameter and see if you get 0.111? And > are you able to extract the timescale of this process (the methyl > group rotamer jumps)? From memory, someone has optimsed these models > using a grid search. This coarse optimisation can be performed in > relax as you are able to specify the fine details of the grid search. > It is slower, but will do the job. You could even implement a zooming > grid search if your scripting skills are up to it to be able to > relatively quickly find the parameters to high precision. Anyway, I > hope this info helps. > > Regards, > > Edward > > > > > > On 6 April 2011 17:39, Tiago Pais <[email protected]> wrote: >> Hi, >> >> I would like to make an analysis of side-chain relaxation data with the > S2f >> parameter (in model 5) set to 0.111. >> >> Is it possible to do this with RELAX? How? >> >> Thanks in advance. >> >> Cheers >> >> Tiago P >> >> >> >> ************************************** >> >> Tiago Pais, PhD. student >> >> Cell Physiology & NMR >> >> Instituto de Tecnologia Química e Biológica-Oeiras >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> [email protected] >> >> 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 >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __________ Information from ESET NOD32 Antivirus, version of virus signature database 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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
