Maik > I just found a strange behaviour of GROMACS, when processing topologies > with B-values. Maybe I just think of it as unintuitive/bug, but here we go: > > e.g. OPLS > > Consider an angle given (all atoms have B-values, which angle-parameter > can be found by GROMACS in the bonded.itp for the A- and B-state): > > Original topology entry: > 10 12 14 1 > > Manually edited entry (with the correct ff-term): > 10 12 14 1 109.700 669.440 > > Now, a dump from the tpr-files yields the following: > Original: > functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= > 1.09500e+02, ctB= 2.92880e+02 > > Edited: > functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= > 1.09700e+02, ctB= 6.69440e+02
I *think* this behavior is described in the documentation. Basically, anytime A state parameters are specified in the topology and B state are omitted, A state are copied to B state. To make B state different, you have to either (a) specify them explicitly, or (b) have them looked up in the force field where they are different. So this is expected behavior. David > Now, what obviously happens is, that GROMACS searches the entries of the > angle in the FF for both states and uses them in the case of the > original topology. > If one puts a manual entry into the topology for the A-state though, the > B-state is simply copied, instead of searched by GROMACS. > > This, IMHO, is quite inconvenient. Is this a bug or a feature? > > Regards > > -- > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php