Hi
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
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/
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