@ Charles Thanks for the feedback. I saw the setting but it didn't quite sink in that it would fix the problem. Guess my thought pattern was stuck in a local minimum.
@ Geoff A good thought. I managed to avoid exploding forces at least, and the dynamics were actually completing. I'll give the force constant adjustment a try anyway and see how it goes. Josh On Nov 15, 2010, at 4:05 PM, Mueller, Geoffrey (NIH/NIEHS) [E] wrote: > Clearly that was a problem. > > Another issue may be if you have very large couplings you may also > create very large forces on the atoms, and you will need to > rebalance (probably lower) the RDC force constants. You may need to > make the time step shorter, and refine longer, similar to Choy et > al. Journal of Biomolecular NMR, 21: 31-40, 2001. > > Cheers, > Geoff > > > On 11/15/10 4:40 PM, "Charles at schwieters.org" > <Charles at schwieters.org> wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Jos-- > >> I am trying to refine a structure of ubiquitin using some very large >> RDCs (several > 100 Hz). During refinement, the rdc energy becomes >> very large, and final structures are yielding 10 out of 40 rdcs >> violated. Looking at the list, all violated residues have observed >> RDC >> greater than 100 and a calculated RDC of exactly 100, so it looks >> like >> you have a maximum value limit in place. All other RDCs are modeled >> quite well. >> >> Is there indeed an upper limit restriction on RDC_calc, and is >> there a >> way that I can increase it? I haven't spotted an appropriate keyword >> in the examples and docs yet. >> > > There is indeed an upper bound for Da which can be adjusted using the > setDaMax method of VarTensor. For example, the setup of the alignment > tensor object in eginput/gb1_rdc/refine.py can be modified as below to > set a maximum Da value to 200 Hz. This is documented here: > http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/varTensor.html > and the default value of DaMax is 50. > > best regards-- > Charles > > # medium Da rhombicity > for (medium,Da,Rh) in [ ('t', -6.5, 0.62), > ('b', -9.9, 0.23) ]: > oTensor = create_VarTensor(medium) > oTensor.setDaMax(200) > oTensor.setDa(Da) > oTensor.setRh(Rh) > media[medium] = oTensor > pass > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/ > ><http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkzhmskACgkQPK2zrJwS/lYXjQCfbo7hJQ0tv0soWOtiACeb+PeC > IDsAn07sAMAIBz00bCBkNUZQ3vM2Gc+T > =MVFI > -----END PGP SIGNATURE----- > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > > -- > Geoffrey A. Mueller, Ph.D. > Staff Scientist, NIEHS > 919-541-3872 > mueller3 at niehs.nih.gov
