Marc F. Lensink wrote:
On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote:
The .mdp file seems reasonable. QM charges are not necessarily the end
result in Gromos parameterization. In fact, such calculations are often
unnecessary. In my experience, assigning charges based on functional groups
already present in the force field is often a reasonable starting point.
But in any case, you must always verify your results and, in the end,
follow the same parameterization scheme as the original force field (which,
in the case of the Gromos force fields, does not include QM charge
calculations).
I've run hundreds of QM charge calculations. in many cases, they are
remarkably similar to the gromos charges...
Agreed. The point I was trying to make (perhaps poorly) was that simply running
a QM charge calculation and calling it done is not the right track. I got the
impression from the original post that charges were assigned and a simulation
conducted without any validation of those parameters.
-Justin
cheers,
marc
_______________________________________________
gmx-users mailing list [email protected]
http://lists.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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.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
