Justin A. Lemkul wrote:
Chih-Ying Lin wrote:
Hi
How to set up the pH value ?
what ions should I put in the solution?
The "pH" of your simulation is governed by the protonation state you
assign to each of the titratable residues in your protein or other
molecules of interest. There is no explicit representation of hydronium
ions in the force fields available in Gromacs. Furthermore, the
presence of hydronium would require acid-base chemistry (proton
transfer) which is not possible under classical mechanics force fields.
But will be soon.
Maybe even in 4.1.
-Justin
Thank you
Lin
------------------------------------------------------------------------
_______________________________________________
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
