[gmx-users] The Cut-off for coulombtype heat up the water system?
dommert at icp.uni-stuttgart.de
Sat Jun 20 03:54:19 CEST 2009
* XAvier Periole <x.periole at 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
> On Jun 19, 2009, at 21:02, Florian Dommert <dommert at icp.uni-
> stuttgart.de> wrote:
>> * Mark Abraham <Mark.Abraham at anu.edu.au> [2009-06-19 14:55:02 +1000]:
>>> Chih-Ying Lin wrote:
>>>> People conclude that the heating up is normal by using a plain cut-
>>>> 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
>> electrostatic forces with a cutoff and relative dielectric
>> != 1. With the mentionend Ewald methods I should be able to reproduce
>> exactly the same circumstances like in a reaction-field setup. So at
>> moment 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 reaction
>> field method you just have two parameters: the cutoff and epsilon_r.
>> other algorithms require addtionally require the input of an
>> size for used grid in Fourier space and in case of SPME/PME/PPPM also
>> interpolation order. Finally you need to set the splitting paramter
>> correctly, otherwise you will obtain unaccurate forces. So there can
>> a very large error introduced, when applying the wrong parameters to
>> 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
>> long range nature is calculated. Therefore an large error is not
>> 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.
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> Florian Dommert
>> Institute for Computational Physics
>> University Stuttgart
>> Pfaffenwaldring 27
>> 70569 Stuttgart
>> Tel: +49 - 711 / 6856-3613
>> Fax: +49 - 711 / 6856-3658
>> EMail: dommert at icp.uni-stuttgart.de
>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>> !! PGP-ENCODED emails preferred !!
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Institute for Computational Physics
Tel: +49 - 711 / 6856-3613
Fax: +49 - 711 / 6856-3658
EMail: dommert at icp.uni-stuttgart.de
!! GPG-ENCODED emails preferred !!
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Size: 194 bytes
Desc: not available
More information about the gromacs.org_gmx-users