... my previous response bounced because of the too large attachment -- I've shortened the output file a bit, just kicked out some repetitive sections. Hope it gets through now...
Hi Charles, Charles at Schwieters.org wrote: >> There still is something missing from my Torsion dynamics setup and I >> am running out of ideas. I added potential terms (although there seems >> to be a problem with the RAMA potential terms, see below). The system >> simulates and prints out energies but, eventually, nothing seems to >> move: >> > > Do the energies change in time? Do they have reasonable values? What are > you trying to accomplish with this calculation? > We want to sample the relative motion of two structured domains that are connected by an unstructured linker. Residues 1 - 107 are domain 1, 122-338 domain 2 and the linker stretch in between is supposed to move freely: dyn = ivm.IVM() dyn.group( AtomSel( 'resid 1:107' ) ) dyn.group( AtomSel( 'resid 122:338') ) The energies seem kind of OK, except perhaps the RAMA term. The last two energy reports look like this: *--- Dynamics ---- step= 180 ---- time= 0.97852 ---- delta_t= 0.010497 --* | E(kin)+E(poten)= -2584.555 E(kin)= 35.534 temperature= 550.204 | | E(poten)= -2620.0888814 grad= 25.7826238 ANGL= 23.5136203 | | BOND= 3.4171185 CDIH= 0.0000000 IMPR= 4.5083458 | | RAMA= -2634.7135214 VDW= -16.8144445 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 183 ---- time= 1.0077 ---- delta_t= 0.0081977 --* | E(kin)+E(poten)= -2586.583 E(kin)= 33.142 temperature= 513.163 | | E(poten)= -2619.7247593 grad= 25.8173762 ANGL= 23.5136203 | | BOND= 3.4171185 CDIH= 0.0000000 IMPR= 7.5138461 | | RAMA= -2636.8811015 VDW= -17.2882427 | *------------------------------------------------------------------------------* De-aktivating the RAMA term doesn't change things though. I am attaching the full log file (dynamics at the end) and the script. It's very likely that I am overlooking something crucial here. For some reason, the energies look very different (unreasonably high with high T) when I am re-initializing the system from the PDB that is created in the first half of the protocol. But I guess that's an unrelated problem that I first have to look into a bit better. Thanks! Greetings, Raik > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkpZu48ACgkQPK2zrJwS/lbMLACbBgsMaiAaKGVr4GhFDsIkKEa9 > qkAAn1hnOojca1HmvDnD/EOOiWdf+MzF > =A+tk > -----END PGP SIGNATURE----- > -- ________________________________ Dr. Raik Gruenberg http://www.raiks.de/contact.html ________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: rb_setup_dynamics.xp.py Type: text/x-python Size: 2940 bytes Desc: not available Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090712/eebce4d8/attachment-0001.py -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: rb_setup_dynamics.out Url: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090712/eebce4d8/attachment.ksh
