[gmx-users] topology treatment in free energy calculations - possible bug

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Jan 4 15:15:57 CET 2008


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:
functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 
1.09500e+02, ctB= 2.92880e+02

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?


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

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