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<div class="moz-cite-prefix">Hi,<br>
<br>
I am sorry to hear about your unfortunate run setup.<br>
<br>
I will put a note on the deprecation and a warning for large
switching range in 4.6.2.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/07/2013 10:41 AM, Michel Cuendet wrote:<br>
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<div>Dear Berk,</div>
<div><br>
</div>
<div>Thanks for your immediate reply. And I apologize for not
providing the relevant cutoffs. Indeed I had a long switching
range. </div>
<div><br>
</div>
<div>OK Whow. So it is exactly as I feared, all my simulations
are flawed. Being a big proponent of energy conservation, when
4.5 came out, I thought PME-switch was like the new
state-of-the-art scheme (without properly checking what it was
doing, my bad...). Now I realize that it is not. It is even
quite wrong, as it probably introduces a sign reversal in the
force around rcoulomb. As you mentioned, switching can be
attained in a safe and consistent way using ewald_rtol. </div>
<div><br>
</div>
<div>It seems to me that the PME-switch option is very
dangerous. As you suggest I think it should be deprecated or
at least it should be accompanied with a serious warning. </div>
<div><br>
</div>
<div>Thanks for your help, </div>
<div>Michel</div>
<div><br>
</div>
<div><br>
</div>
<div>On Mar 6, 2013, at 7:34 PM, <a moz-do-not-send="true"
href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>
wrote:</div>
<blockquote type="cite">
<div>Message: 4<br>
Date: Wed, 06 Mar 2013 19:29:19 +0100<br>
From: Berk Hess <<a moz-do-not-send="true"
href="mailto:hess@kth.se">hess@kth.se</a>><br>
Subject: Re: [gmx-developers] PME-Switch vs. PME<br>
To: Discussion list for GROMACS development<br>
<span class="Apple-tab-span" style="white-space:pre"> </span><<a
moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:51378AFF.9020201@kth.se">51378AFF.9020201@kth.se</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
<br>
You don't mention your, critical, cut-off parameters.<br>
I guess you used a long switching range. The switch is only
intended to <br>
avoid<br>
cut-off artifacts (and therefore does not act on the
reciprocal).<br>
<br>
Any switching function should only be applied over a very
short range.<br>
As with PME ewald_rtol is usually 10^-5, you don't really
need the switch,<br>
and if you do want to use it, you should switch over 0.05 nm
or less.<br>
<br>
But in 4.6 you can use exact cut-off's, either with the
Verlet cut-off <br>
scheme,<br>
or at a high cost also with the group cut-off scheme. Thus
PME-switch is <br>
no longer needed<br>
and we should deprecate it in 4.6.<br>
<br>
Cheers,<br>
<br>
Berk<br>
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<div>==========================================================</div>
<div>Michel Cuendet, PhD</div>
<div>Molecular Modeling Group</div>
<div>Swiss Institute of Bioinformatics</div>
<div>CH-1015 Lausanne</div>
<div>Switzerland</div>
<div><a moz-do-not-send="true"
href="http://lausanne.isb-sib.ch/%7Emcuendet/">http://lausanne.isb-sib.ch/~mcuendet/</a></div>
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