<div dir="ltr">Berk (and all),<br><br><br><div class="im">On Thu, May 2, 2013 at 12:54 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<div>This is all describes in the manual,
AFAIK.<div><br></div></div></div></blockquote></div><div>Sorry there was some overlap. I hadn't found the discussion I'll cite below yet. <br></div><div class="im"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"><div><div>
On 05/02/2013 09:44 PM, David Mobley wrote:<br>
</div></div><div>
<blockquote type="cite">
Right, what I'm asking about is
<div>A) how exactly is this end result <span></span>achieved? (The
system is periodic, so how is the periodicity removed for the
end state?)</div>
</blockquote></div>
The periodicity of intra-molecular interactions is always removed.<br>
These interactions are excluded from PME and added directly as
listed pairs.</div></blockquote><div><br></div></div><div>The manual says this: "<span style="font-size:11pt;font-family:'NimbusRomNo9L'">All intra-molecular non-bonded interactions for moleculetype </span><span style="font-size:11pt;font-family:'NimbusMonL'">couple-moltype
</span><span style="font-size:11pt;font-family:'NimbusRomNo9L'">are replaced by exclusions and explicit pair interactions. In this manner the decou-
pled state of the molecule corresponds to the proper vacuum state without periodicity
effects.
</span>
"<br><br></div><div>Does this apply to BOTH the A and B states? Your
answer "the periodicity of intra-molecular interactions is always
removed" suggests you're saying that the solute is never allowed (in
either A or B state) to interact with copies of itself. Doesn't this
mean that that (considering the case of a small molecule in solution
being decoupled) the A state has periodic interactions between all of
the solvent molecules, and between solvent and solute, but no periodic
interactions between solute and solute? (If so, won't this tend to leave
the solvent box with a net dipole moment for PME purposes?) <br>
</div><div class="im"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF"><div><br>
<blockquote type="cite">
<div>B) how was it validated that it is working as it should be?</div>
</blockquote></div>
I checked this and it works.</div></blockquote><div><br></div></div><div>What
I'm asking is, "checked how", and "works for what"? Specifically I'm
trying to figure out whether this can be expected to always yield the
same results as annihilation (assuming simulations are converged), even
for larger/flexible/more polar molecules. To that end I'm trying to
understand whether there are any limitations in the formalism, and
exactly how it's been tested.<br>
</div><div class="im"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF"><div><br>
<blockquote type="cite">
<div>C) when you say, "without cutoffs", is this referring to just
Coulomb cutoffs or also LJ? I'm assuming just coulomb. If so,
then there are internal LJ interactions in the gas phase which
are missing outside the LJ cutoff (assuming the molecule is
larger than the cutoff). While these are also missing in
solution, they are generally captured well by the dispersion
correction. In vacuum that is not the case, so neglect of these
could adversely affect solvation estimates, it seems to me. Has
this been tested? How?</div>
</blockquote></div>
LJ is treated as Coulomb, plain LJ, no cut-off.<div><br></div></div></blockquote></div><div>OK, thanks. <br></div><div class="im"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"><div>
<blockquote type="cite">
<div>D) how will the use of decoupling affect dispersion
corrections to the energy and pressure? (Will the dispersion
corrections still give the correct free energy contribution in
decoupling?) how has this been tested, if at all?</div>
</blockquote></div>
This is the only complicating factor.<br>
There is no correct way of using dispersion correction with
decoupling.<br>
As the intra-molecular interactions are excluded, these do not end
up the average C6<br>
and they do not end up in the pair count for dispersion correction.<br></div></blockquote><div><br></div></div><div>So,
are you saying dispersion corrections should be turned off when using
decoupling? Dispersion corrections tend to contribute substantially to
free energies unless one runs with a large cutoff, which would suggest
this is a bad idea. It seems like I probably need to know exactly how
the dispersion correction contribution to the free energy is computed in
the case of decoupling, so I can estimate how wrong this will be due to
the pair count/average C6 being wrong. <br>
<br></div>Probably this also raises the question of whether GROMACS
should not allow the user to run decoupling with the dispersion
correction (since it's not correct) or whether it instead should issue a
warning and provide some guidance as to how to fix things (if we have
any such guidance to offer).<br>
<br>Thanks,<br>David</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, May 2, 2013 at 12:54 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>This is all describes in the manual,
AFAIK.<div class="im"><br>
<br>
On 05/02/2013 09:44 PM, David Mobley wrote:<br>
</div></div><div class="im">
<blockquote type="cite">
Right, what I'm asking about is
<div>A) how exactly is this end result <span></span>achieved? (The
system is periodic, so how is the periodicity removed for the
end state?)</div>
</blockquote></div>
The periodicity of intra-molecular interactions is always removed.<br>
These interactions are excluded from PME and added directly as
listed pairs.<div class="im"><br>
<blockquote type="cite">
<div>B) how was it validated that it is working as it should be?</div>
</blockquote></div>
I checked this and it works.<div class="im"><br>
<blockquote type="cite">
<div>C) when you say, "without cutoffs", is this referring to just
Coulomb cutoffs or also LJ? I'm assuming just coulomb. If so,
then there are internal LJ interactions in the gas phase which
are missing outside the LJ cutoff (assuming the molecule is
larger than the cutoff). While these are also missing in
solution, they are generally captured well by the dispersion
correction. In vacuum that is not the case, so neglect of these
could adversely affect solvation estimates, it seems to me. Has
this been tested? How?</div>
</blockquote></div>
LJ is treated as Coulomb, plain LJ, no cut-off.<div class="im"><br>
<blockquote type="cite">
<div>D) how will the use of decoupling affect dispersion
corrections to the energy and pressure? (Will the dispersion
corrections still give the correct free energy contribution in
decoupling?) how has this been tested, if at all?</div>
</blockquote></div>
This is the only complicating factor.<br>
There is no correct way of using dispersion correction with
decoupling.<br>
As the intra-molecular interactions are excluded, these do not end
up the average C6<br>
and they do not end up in the pair count for dispersion correction.<br>
<br>
Cheers.<span class="HOEnZb"><font color="#888888"><br>
<br>
Berk</font></span><div><div class="h5"><br>
<blockquote type="cite">
<div><br>
</div>
<div>Thanks!<br>
<br>
On Thursday, May 2, 2013, Berk Hess wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
You didn't explain exactly what you are doing.<br>
The decouple mdp options decouple the molecule to a vacuum
state, i.e. pure Coulomb without cut-off's.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 05/02/2013 07:10 PM, David Mobley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Could I get some input on this?<br>
<br>
I have a couple of cases for rather polar molecules
where decoupling and annihilation give me statistical
significant differences in hydration free energies. The
differences are not that large, but significant. I'm
trying to find out what's already been done to validate
so I know how much time/effort to spend testing to try
and figure out if there is a problem here.<br>
<br>
Thanks.</div>
<div><br>
<br>
<div>On Tue, Apr 30, 2013 at 1:25 PM, David van der
Spoel <span dir="ltr"><<a>spoel@xray.bmc.uu.se</a>></span>
wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 2013-04-30 18:02, David Mobley wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Hi,<br>
<br>
In GROMACS 4.6 and later, there's now a new
feature available to allow<br>
decoupling of solute molecules in free energy
calculations. I wanted to<br>
inquire as to how Coulomb decoupling works, as
I'm not clear.<br>
<br>
Specifically, imagine I'm running a calculation
of the hydration free<br>
energy of a small molecule in water, and I
decouple it (LJ and Coulomb)<br>
from its surroundings. What is the final
reference state for the small<br>
molecule? Is it the small molecule interacting
with periodic copies of<br>
itself in the gas phase (bad)? Or is it not
interacting with periodic<br>
copies of itself either? If the latter, how is
this achieved?<br>
</blockquote>
</div>
Good question, also one would like to be able to
decouple a molecule only in the central box and not
in the surrounding boxes. This does not make a
difference for liquids but it does for crystals.<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div> <br>
Since I'm not familiar with the Coulomb
decoupling aspect and it is<br>
conceptually more complicated than LJ
decoupling, I want to make sure I<br>
understand how it's supposed to be working.<br>
<br>
Thanks!<br>
David<br>
<br>
<br>
--<br>
David Mobley<br>
</div>
<a>dmobley@gmail.com</a>
<mailto:<a>dmobley@gmail.com</a>><br>
<a value="+19493852436">949-385-2436</a><br>
<br>
<br>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> <br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala
University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a value="+46184714205">+46184714205</a>.<br>
<a>spoel@xray.bmc.uu.se</a>
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<br>
-- <br>
David Mobley<br>
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</blockquote>
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</blockquote>
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<br>
<br>
-- <br>
Sent from my mobile device. Please pardon any unusual brevity or
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</blockquote>
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