Hi Erik,
Erik Lindahl wrote:
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs. Rather,
Erik Lindahl started the implementation of this stuff but did never
finish it completely, due to other priorities I presume. We should
however take out the variables to avoid confusion (unless someone
provides a full implementation).
Actually, technically the GB implementation is already in Gromacs (even
assembly kernels), and quite correct, it's just that you don't have the
born radii yet :-)
I can't find any usage of the GB parameters as read from the mdp file -
neither in the latest release nor the HEAD revision in the CVS. Is there
another branch in the CVS you got that code in?
I'm just curious as we worked on some GB models as well and using (at
least the STILL) with assembly loops sounds very nice to me.
Somewhat unrelated: I also saw the andersen_seed parameter and I was
wondering if there is a code branch that contains an Andersen thermostat?
Cheers,
Edgar
--
Edgar Luttmann, PhD
Stanford University, Stanford, CA, USA
Department of Chemistry, Group of Prof. Dr. V. Pande
postdoctoral researcher: [EMAIL PROTECTED] - distributed computing
Clark Center, 94305-5080 Stanford, CA, phone: (650) 723 1097
email: luttmann AT stanford.edu, www: http://www.stanford.edu/~luttmann
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
