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<div class="moz-cite-prefix">Hi!<br>
<br>
thanks for commenting. The authors address both the pressure and
the free-energy artifacts due to the neutralizing
plasma/background charge in PME simulations. So the pressure
artifact was also considered in the protein example, and the
proposed correction was able to significantly decrease both.<br>
<br>
In the meantime I am aware of the artifacts you mention and I
assume you are right and better suited than me to assess the
advantages of such a correction. I only would like to simulate a
charged, hydrated membrane system if there is no objections
against that from a theoretical point of view (to find this out
was the original goal of these postings), and if there is a
corresponding implementation in Gromacs, what is not the case.
Therefore I will add counter ions or otherwise neutralize the
system, as usual. Nevertheless, it would be nice to have an
ion-free reference state to compare with systems containing salt
and so better assess the effect of the ions.<br>
<br>
Best,<br>
<br>
Felipe<br>
<br>
On 11/12/2012 12:46 PM, Gerrit Groenhof wrote:<br>
</div>
<blockquote cite="mid:3760091B-14D7-49EB-8652-FD155D77C9F1@gwdg.de"
type="cite">Hi,
<div><br>
</div>
<div>But they did not look at the free energy profile of an ion
moving across the system, only total electrostatic energy in
these two cases. </div>
<div><br>
</div>
<div>In a true non-homegenous system, such as lipid bilayer in
water, you will see artefacts if the system is non-neutral, with
the free energy of the ion inside the lower dielectric either
too high or too low, depending on the signs and magnitudes of
the ion and net charge in the system. We have not tried, but I
don't see how the correction would alleviate that problem. In
their scheme, the correction term would be independent of the
position of the test particle.</div>
<div><br>
</div>
<div>It is not clear to me why you want to simulate a net charged
system. Can't you avoid this by adding counterions?</div>
<div><br>
</div>
<div>Gerrit</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>On Nov 12, 2012, at 1:06 PM, Felipe Pineda, PhD wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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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">
<meta http-equiv="content-type" content="text/html;
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>
========================================
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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 moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:luis.pinedadecastro@lnu.se">luis.pinedadecastro@lnu.se</a>|
| Web: <a moz-do-not-send="true" href="http://lnu.se">lnu.se</a> |
+-----------------------------------+</pre>
</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
<br>
<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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