* XAvier Periole <x.peri...@rug.nl> [2009-06-20 00:45:55 +0200]:
It is simply that if the system is not neutral the Ewald equation are not valid anymore. I would guess that the original papers describe it. I never looked into it.
Thanks very much. This should really be the point, because a lattice built just of like-charged ions would have infinite energy. So this reason should suffice to explain why Ewald can not be applied in such cases. Flo
On Jun 19, 2009, at 21:02, Florian Dommert <domm...@icp.uni- stuttgart.de> wrote:* Mark Abraham <mark.abra...@anu.edu.au> [2009-06-19 14:55:02 +1000]:Chih-Ying Lin wrote:HiPeople conclude that the heating up is normal by using a plain cut- off.So, how to fix the problem?0. Do more background reading. :-)1. From Berk => use multiple groups. => how ??? => I have been thinking that it is better to group the molecule => such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? => such as PME, PPPM ? => what's the suggestion about this? 3. Normally, how do people fix this problem?These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme.Hi Mark, Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ?When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity!= 1. With the mentionend Ewald methods I should be able to reproduceexactly the same circumstances like in a reaction-field setup. So at themoment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in order to obtain an appropriate accuracy of the forces. In the reactionfield method you just have two parameters: the cutoff and epsilon_r. The other algorithms require addtionally require the input of an appropriate size for used grid in Fourier space and in case of SPME/PME/PPPM also aninterpolation order. Finally you need to set the splitting paramtercorrectly, otherwise you will obtain unaccurate forces. So there can be a very large error introduced, when applying the wrong parameters to the Ewald methods. The heat up of the water is also just related to extremly inaccurate electrostatic forces, since with PBC an "infinite" system is simulated and just a very small amount of the electrostatic interaction that is of long range nature is calculated. Therefore an large error is not unexpected.Finally the only restriction of Ewald I see is the requirement of PBC, where I can reach any level of accuracy for the electrostatic force given by certain charge distribution, don't I ? However I am always open to enhance my experience and knowledge therefore please let me know if understood anything wrong. FloMark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 thewww interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! GPG-ENCODED emails preferred !!
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