Berk
Thanks for the clarification.
I was aware of A-values copied to B-values, when no B-values in the FF
exist, but actually this was new to me.
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/
Berk Hess wrote:
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.
Berk.
From: Maik Goette <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: GMX-mailinglist <gmx-users@gromacs.org>
Subject: [gmx-users] topology treatment in free energy calculations
-possible bug
Date: Fri, 04 Jan 2008 15:15:57 +0100
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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