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<div class="moz-cite-prefix">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 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 scheme,<br>
or at a high cost also with the group cut-off scheme. Thus
PME-switch is no longer needed<br>
and we should deprecate it in 4.6.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 03/06/2013 07:13 PM, Michel Cuendet wrote:<br>
</div>
<blockquote
cite="mid:CDC29353-F5EB-4832-B95B-E64136CA42AE@isb-sib.ch"
type="cite">
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<br>
Hi, <br>
<br>
I tried to compare PME and PME-switch for a small peptide in
solution with Amber96. I was surprised to see that when
introducing the Switch function, only the real-space energy is
affected, whereas the reciprocal-space part is not. The difference
in total energy is huge, about 4919 kJ/mol for my system. Below
are the numbers. Shouldn't the reciprocal energy be "switched" as
well, in the spirit of what the error function does in Eq. (4.160)
and (4.161) of the 4.6.1 manual?<br>
<br>
Unfortunately, the energy is not just shifted by a constant.
Comparing two different conformations with PME and PME-Switch
gives me a DeltaDeltaE of the order of 58 kJ/mol. I also compared
the energies with Amber12, and found that PME reproduced the Amber
electrostatics within 21 kJ/mol, with a DeltaDeltaE below 2 kJ/mol
comparing the two conformations in gromacs and Amber12.<br>
<br>
I ran extensive simulations of this peptide with gromacs 4.5.5 and
PME-Switch (using various enhanced sampling methods). The peptide
would never stay folded, whereas it has been reported to have a
significant folded population in simulations with the same force
field and cutoffs done with the Amber8 package. Do you think this
could be due to the altered electrostatics? I can't see any other
explanation at the moment. <br>
<br>
<br>
Gromacs 4.5.5 PME :<span class="Apple-tab-span"
style="white-space:pre"> </span><br>
Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>2898.323974<br>
Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre">
</span>-221730.3613<br>
Coul. recip.<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.81872<br>
Potential<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>-204582.3431<br>
<span class="Apple-tab-span" style="white-space:pre"> </span> <br>
Gromacs 4.5.5 PME-Switch :<span class="Apple-tab-span"
style="white-space:pre"> </span><br>
Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>2898.323974<br>
Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre">
</span>-226649.5443<span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span>difference = -4919.1830<br>
Coul. recip.<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.81872<br>
potential<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>-209501.5261<br>
<span class="Apple-tab-span" style="white-space:pre"> </span> <br>
Gromacs 4.6.1 PME, coulomb-modifier=none<br>
Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>2898.32373<br>
Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre">
</span>-221730.4063<br>
Coul. recip.<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.46875<br>
potential<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>-204592.1719<br>
<br>
Gromacs 4.6.1 PME-switch, coulomb-modifier=none<br>
Coulomb-14<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>2898.32373<br>
Coulomb (SR)<span class="Apple-tab-span" style="white-space:pre">
</span>-226649.625<span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span><span class="Apple-tab-span"
style="white-space:pre"> </span>difference = -4919.2188<br>
Coul. recip.<span class="Apple-tab-span" style="white-space:pre">
</span><span class="Apple-tab-span" style="white-space:pre"> </span>-24396.46875<br>
potential<span class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span><span
class="Apple-tab-span" style="white-space:pre"> </span>-209511.3906<br>
<br>
<br>
I can send files and more elaborate data if required.<br>
<br>
Thanks and kind regards,<br>
Michel<br>
<br>
<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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