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<div class="moz-cite-prefix">Hi,<br>
<br>
thanks for the useful comments. I have checked the paper again and
it tuns out that they did test the correction also on a
inhomogeneous system:<br>
<br>
<i>To</i><i> </i><i>further illustrate the effects of charge on
the Ewald method</i><i><br>
</i><i>we have performed similar calculations on two other systems</i><i><br>
</i><i>in vacuo: a deprotonated acetate molecule and sperm whale</i><i><br>
</i><i>myoglobin protein. Calculations of the electrostatics both</i><i><br>
</i><i>with and without the net-charge correction on this protein</i><i><br>
</i><i>system tests the validity of correcting the net-charge
interactions</i><i><br>
</i><i>with a simple point charge calculation on a system</i><i><br>
</i><i>much more complex than the three-ion system.</i><br>
<br>
Since the proposed correction seems to be implemented only in
CHARMM version 25 and refined in version 26, and not in Gromacs,
it's not relevant for me from a pragmatical point of view.<br>
<br>
Kind regards,<br>
<br>
Felipe<br>
<br>
On 11/08/2012 12:11 PM, Gerrit Groenhof wrote:<br>
</div>
<blockquote cite="mid:48C07DE5-4580-462C-87E7-2E13520FB4B9@gwdg.de"
type="cite">Hi,
<div><br>
</div>
<div>The net-charge correction by B. Brooks and co-workers
corrects for total energy and pressure artefacts only in
homogeneous systems as far as I understand it.</div>
<div><br>
</div>
<div>However, there are serious artefacts on the free energy
profiles (and thus partitioning) of charged particles in boxes
with inhomogeneous dielectric media (such as proteins, lipid
bilayers, and almost everything else that is biologically
relevant). These artefacts cannot be corrected by the
aforementioned approach. Only explicit neutralization by means
of counter ions can lead to meaningful results.</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Gerrit</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><br class="Apple-interchange-newline">
<blockquote type="cite">
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charset=ISO-8859-1">
<div text="#000000" bgcolor="#FFFFFF"> -------- Original
Message --------
<div class="moz-forward-container">
<div class="moz-forward-container">
<table class="moz-email-headers-table" border="0"
cellpadding="0" cellspacing="0">
<tbody>
<tr>
<th nowrap="nowrap" valign="BASELINE"
align="RIGHT">Subject: </th>
<td>Re: [gmx-users] Simulation of charged
systems (2)</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE"
align="RIGHT">Date: </th>
<td>Tue, 6 Nov 2012 18:21:57 +0100</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE"
align="RIGHT">From: </th>
<td>Justin Lemkul <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE"
align="RIGHT">To: </th>
<td>Luis Felipe Pineda de Castro <a
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:luis.pinedadecastro@lnu.se"><luis.pinedadecastro@lnu.se></a></td>
</tr>
</tbody>
</table>
<br>
<br>
<pre>(Replied off-list)
I think it would be more productive to post this to gmx-developers rather than
gmx-users, since it really is an inquiry about the code itself. The core
developers usually don't reply to gmx-users, and they're the ones who will have
the answers. My inclination is that the answer to your question (now that it's
more clear what you're asking) is "no," but since I have no direct knowledge of
the PME code, I can't say for certain.
-Justin
On 11/6/12 3:27 AM, Felipe Pineda, PhD wrote:
> Hi,
>
> thanks to Justin for the pointer to the list archive I searched before with "net
> charge", but without getting useful results. For the sake of clarity, I am not
> referring to the "neutralizing plasma" or neutralizing background charge used
> implicitly with PME, but to an additional net-charge correction implemented for
> example in CHARMM to avoid, at least partly, the artifacts produced by that
> neutralizing background charge in net-charged systems, which are sometimes
> unavoidable (s., eg., Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and
> free energy artifacts in charged periodic systems via net charge corrections to
> the ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84.
> <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1"><http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1></a>).
>
> Felipe
>
> On 11/05/2012 02:27 PM, Justin Lemkul wrote:
>>
>> On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote:
>>> Hi again!
>>>
>>> many thanks to Xavier for his response, the only one I got so far ... I had the
>>> same impression, but I'm seeking for theoretically/technically more funded
>>> statements. My impression is also that there are different kind of "equations"
>>> depending of the treatment of long-range electrostatic interactions.
>>>
>>> My concrete question is now: are net charge corrections to the Ewald potential
>>> implemented in Gromacs?
>>>
>> <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html">http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html</a>
>>
>> Searching the list archive for "neutralizing background charge" turns up a large
>> number of results. This is a fairly common question, and there are many replies
>> with varying degrees of detail.
>>
>> -Justin
>>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
========================================
</pre>
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<pre class="moz-signature" cols="72">--
+-----------------------------------+
| Luis Felipe Pineda De Castro, PhD |
| Computational Chemist - Postdoc |
| Computational Chemistry and |
| Biochemistry Laboratory |
| School of Natural Sciences |
| Linnaeus University |
| SE-391 82 Kalmar |
| Norrgård, room 311 |
| Sweden - Sverige |
| Phone: ++46-480-44 6329 |
| Mobile: ++46-76-8420572 |
| E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:luis.pinedadecastro@lnu.se">luis.pinedadecastro@lnu.se</a>|
| Web: lnu.se |
+-----------------------------------+</pre>
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