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

Berk Hess gmx3 at hotmail.com
Fri Jan 4 16:37:03 CET 2008

This behavior is itentional.
But it can indeed be confusing.
Therefore in Gromacs 4.0 a warning will be generated (and I have added
a table in the manual that explains all the possible combinations).

If you explicitly define parameters for the A-state, I don't see why
you would want the B-parameters to be looked up based on atom-type.
You would only want that when the A-state parameters are also determined
by the atom type.


>From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: GMX-mailinglist <gmx-users at gromacs.org>
>Subject: [gmx-users] topology treatment in free energy calculations 
>-possible bug
>Date: Fri, 04 Jan 2008 15:15:57 +0100
>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 
>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
>         mgoette2[at]gwdg.de
>WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
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