[gmx-users] topology treatment in free energy calculations - possible bug_2nd

[David Mobley]

Maik,

> It just came to my mind, that the behaviour, I described in the first
> mail will be quite dangerous, whenever #define statements are in the
> topology, cause this would lead to the insertion of the FF-values in the
> topology, when preprocessing, and then be copied into the B-state
> afterwards, even if the values are crap for the B-state...

As far as treatment of A and B state parameters, I am not sure there
is any solution that doesn't result in "dangerous" behavior in some
situations. Therefore my recommendation is that anytime one is
handling atoms which are being perturbed (i.e., where the B state
*might* be different from the A state) both A and B state parameters
be specified explicitly in the topology by the user.

David


> 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/
>
>
> --
> 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
>