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

[David Mobley]

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 at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>