Thanks for the detailed reply. This is a really good example for the
manifold of traps you can tap into when treating long range forces.
Flo
* Mark Abraham mark.abra...@anu.edu.au [2009-06-20 14:55:39 +1000]:
Florian Dommert wrote:
* Mark Abraham mark.abra...@anu.edu.au [2009-06-20 11:54:46
Sorry I habe to extend this:
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
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.
On Jun 19, 2009, at 21:02, Florian Dommert domm...@icp.uni-
stuttgart.de wrote:
* Mark Abraham mark.abra...@anu.edu.au
* 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
Florian Dommert wrote:
* Mark Abraham mark.abra...@anu.edu.au [2009-06-19 14:55:02 +1000]:
Chih-Ying Lin wrote:
Hi
People 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.
* Mark Abraham mark.abra...@anu.edu.au [2009-06-20 11:54:46 +1000]:
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 reproduce
exactly the
Dear Justin:
Thanks for your response.
The reason I am doing this is that I wanted to test what the different
electrostatics treatments will affect my results. So the heating up is
normal by using a plain cut-off and the results can not be trusted, right?
On Wed, Jun 17, 2009 at 5:20 PM, Justin
Yanmei Song wrote:
Dear Justin:
Thanks for your response.
The reason I am doing this is that I wanted to test what the different
electrostatics treatments will affect my results. So the heating up is
normal by using a plain cut-off and the results can not be trusted, right?
On Wed, Jun 17,
Yanmei Song wrote:
Dear Justin:
Thanks for your response.
The reason I am doing this is that I wanted to test what the different
electrostatics treatments will affect my results. So the heating up is
normal by using a plain cut-off and the results can not be trusted, right?
That is one
Dear Justin:
Thank you so much for your answer. That helps a lot!
On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Yanmei Song wrote:
Dear Justin:
Thanks for your response.
The reason I am doing this is that I wanted to test what the different
electrostatics
Hi
People conclude that the heating up is normal by using a plain cut-off.
So, how to fix the problem?
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
Chih-Ying Lin wrote:
Hi
People 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:
Dear Users:
I was running a system by non-equilibrium MD using a plain Cut-off for the
electrostatics:
title = water
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 50 ;
Yanmei Song wrote:
Dear Users:
I was running a system by non-equilibrium MD using a plain Cut-off for
the electrostatics:
title = water
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps
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