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Hello Raik-- > >> 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: The default settings for the Python interface are for structure determination calculations- they are not appropriate for realistic MD calculations. Moreover, you will need some description of the solvent to obtain qualitatively realistic results. You will probably want to replace the RAMA term with the DIHE term. You should not want to call massSetup(). > > *--- 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 > | > *------------------------------------------------------------------------------* > How much motion do you see versus that expected for 1ps of simulation at 500K? > 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. not sure what's going on there. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkpbpIcACgkQPK2zrJwS/lZudwCcCntYixPwtp4Czs3q7UGXY1xi KJsAn0JmBdIpEaxmboA+Q6V7YJ4Uxkt1 =a4lr -----END PGP SIGNATURE-----
