rob yang wrote:
At the risk of exposing my density in triangle geometry here, why does
180-DHA = ADH?
H
/ \
D ----- A
This shows it... I confused it even further. The angle we have been
using since 3.2 is HDA. If 0, it is perfect, if more than 30 (-acut
option) it is not counted anymore.
Sorry for the confusion.
Thank you.
-Rob
> Obviously the DHA angle in a linear Hbond is
> 180, so it should either be 180-DHA or ADH. The ADH angle is what's
> implemented in gromacs > 3.2.1, however in 3.1.4 it still was DHA. The
> default maximum angle has changed from 60 in gmx 3.1.4 (based on Kabsch
> and Sander 1983) to 30 (from 3.2.1 onwards, based on other literature).
> So my paper uses ADH, even though it says DHA.
>
> > Thank you.
> >
> > -Rob
> >
> >
------------------------------------------------------------------------
> > Windows Live Messenger. Multitasking at its finest.
> > <http://www.microsoft.com/windows/windowslive/messenger.aspx>
> >
> >
> >
------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list [email protected]
> > 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 [email protected].
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> [email protected] [email protected] http://folding.bmc.uu.se
> _______________________________________________
> gmx-users mailing list [email protected]
> 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 [email protected].
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
Twice the fun— Share photos while you chat with Windows Live Messenger.
<http://www.microsoft.com/windows/windowslive/messenger.aspx>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
