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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>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> gromacs.org_gmx-developers-bounces@maillist.sys.kth.se <gromacs.org_gmx-developers-bounces@maillist.sys.kth.se> on behalf of Berk Hess <hess@kth.se><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>
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<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 <s1374284@sms.ed.ac.uk> wrote:<br type="attribution">
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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>
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<div dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> gromacs.org_gmx-developers-bounces@maillist.sys.kth.se <gromacs.org_gmx-developers-bounces@maillist.sys.kth.se> on behalf of Berk Hess <hess@kth.se><br>
<b>Sent:</b> 13 September 2016 12:02<br>
<b>To:</b> gmx-developers@gromacs.org<br>
<b>Subject:</b> Re: [gmx-developers] The role of Jacobian factor in alchemical free energy simualtion</font>
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<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>
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<div style="background-color:white"><font color="black" face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt;background-color:white"></span></font><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><font color="black">Dear
Gromacs staff,</font></span></font><br>
<font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"></span></font><font color="black" face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt;background-color:white"></span></font>
<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><br>
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<div><font color="#500050" face="Arial,sans-serif" 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 color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><br>
</span></font></div>
<div><font color="#500050" face="Arial,sans-serif" 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 color="#222222" face="Arial,sans-serif" 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 color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><br>
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<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><br>
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<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><font color="black">Thank you</font></span></font></div>
<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><br>
</span></font></div>
<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><font color="black">Best regards,</font></span></font></div>
<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><br>
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<div><font color="#500050" face="Arial,sans-serif" size="1"><span style="font-size:12.79px"><font color="black">Stefano</font></span></font></div>
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