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<div class="moz-cite-prefix">Hi,<br>
<br>
If this is an "issue" or not depends on what you want to
calculate.<br>
<br>
I have never encountered users that want to change many
constraints lengths in a molecule and also we would in most cases
advise people to only constrain bonds involving hydrogens, so I
don't think this is an important issue.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 09/15/2016 04:10 PM, BOSISIO Stefano wrote:<br>
</div>
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cite="mid:HE1PR05MB1611B822C39018D2FFA0616AE8F00@HE1PR05MB1611.eurprd05.prod.outlook.com"
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<p>Thanks for the answer.</p>
<p>I am still wondering 2 questions:</p>
<p>1) Calculating the Fixman potential could lead to a
correction of this issue?</p>
<p>2) Is Gromacs programmed to correct this issue?<br>
<br>
Thank you very much</p>
<p><br>
</p>
<p>Best,</p>
<p><br>
</p>
<p>Stefano<br>
</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se></a>
on behalf of Berk Hess <a class="moz-txt-link-rfc2396E" href="mailto:hess@kth.se"><hess@kth.se></a><br>
<b>Sent:</b> 13 September 2016 16:54:39<br>
<b>To:</b> Discussion list for GROMACS development<br>
<b>Subject:</b> Re: [gmx-developers] The role of Jacobian
factor in alchemical free energy simualtion</font>
<div> </div>
</div>
<div>
<p dir="ltr">No, all other interactions that work on the bond
length also contribute, i.e. forces from potentials and other
connected constraints.</p>
<p dir="ltr">Cheers,</p>
<p dir="ltr">Berk</p>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sep 13, 2016 5:24 PM, BOSISIO
Stefano <a class="moz-txt-link-rfc2396E" href="mailto:s1374284@sms.ed.ac.uk"><s1374284@sms.ed.ac.uk></a> wrote:<br
type="attribution">
<blockquote class="quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div
style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:'calibri'
, 'arial' , 'helvetica' , sans-serif">
Hi,
<p><br>
</p>
<p>Thanks for the answer. </p>
<p>Thus, taking a constrained bond length, which is
alchemically transformed, the only term that comes
into play is the mass metric tensor, isn't it?<br>
Is there any piece of code of Gromacs which is
designated to correct this issue, you could address
me?</p>
<p><br>
</p>
<p><br>
</p>
<p>Best wishes,</p>
<p><br>
Stefano<br>
</p>
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se></a>
on behalf of Berk Hess <a class="moz-txt-link-rfc2396E" href="mailto:hess@kth.se"><hess@kth.se></a><br>
<b>Sent:</b> 13 September 2016 12:02<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<b>Subject:</b> Re: [gmx-developers] The role of
Jacobian factor in alchemical free energy
simualtion</font>
<div> </div>
</div>
<div>
<div>Hi,<br>
<br>
In alchemical reactions it is often desirable to
avoid changing bond lengths by using a topology
with atoms from both states present. In that case
there is no explicit Jacobian involved. If you do
change constraint lengths, the metric tensor
contribution comes in through the constraint
forces. If you want this effect or not depends on
what quantity you want to calculate exactly. You
can correct for this analytically afterwards.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-09-13 11:57, BOSISIO Stefano wrote:<br>
</div>
<blockquote>
<div
style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:'calibri'
, 'arial' , 'helvetica' , sans-serif">
<div>
<div>
<div>
<div>
<div>
<div dir="ltr">
<div style="background-color:white"><font
face="Calibri,Arial,Helvetica,sans-serif" color="black" size="3"><span
style="font-size:12pt;background-color:white"></span></font><font
face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><font
color="black">Dear Gromacs
staff,</font></span></font><br>
<font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"></span></font><font
face="Calibri,Arial,Helvetica,sans-serif" color="black" size="3"><span
style="font-size:12pt;background-color:white"></span></font>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><br>
</span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><font
color="black">I am trying
to understand some
internal issues between my
code and Gromacs in
alchemical free energy
calculations.</font></span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><br>
</span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><font
color="black">Considering
a simple alchemical free
energy calculation (e.g
ethane to methanol) with a
constraint applied to all
the hydrogen bonds does
Gromacs calculate a
Jacobian correction ? (</font><font
color="black">Boresch
Stefan, and Martin Karplus
"The Jacobian factor in
free energy simulations." </font><font
color="black"><i>The
Journal of chemical
physics</i></font><font
color="black">105.12
(1996): 5145-5154 )</font></span></font></div>
<div><font face="Arial,sans-serif"
color="#222222" size="1"><span
style="font-size:12.79px"><font
color="black">Alternatively,
does Gromacs apply any
correction to the computed
free energy changes if
constraints were applied
to a solute?</font></span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><br>
</span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><br>
</span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><font
color="black">Thank you</font></span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><br>
</span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><font
color="black">Best
regards,</font></span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><br>
</span></font></div>
<div><font face="Arial,sans-serif"
color="#500050" size="1"><span
style="font-size:12.79px"><font
color="black">Stefano</font></span></font></div>
</div>
</div>
</div>
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</div>
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<br>
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<br>
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