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<div class="moz-cite-prefix">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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cite="mid:HE1PR05MB16114FBDD67C855FEDDA10F3E8FE0@HE1PR05MB1611.eurprd05.prod.outlook.com"
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<div id="divtagdefaultwrapper"
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face="Calibri,Arial,Helvetica,sans-serif"
size="3" color="black"><span
style="font-size:12pt;background-color:white;"
id="divtagdefaultwrapper"></span></font><font
face="Arial,sans-serif" size="1" color="#500050"><span
style="font-size:12.79px;"><font color="black">Dear
Gromacs staff,</font></span></font><br>
<font face="Arial,sans-serif" size="1"
color="#500050"><span style="font-size:12.79px;"></span></font><font
face="Calibri,Arial,Helvetica,sans-serif"
size="3" color="black"><span
style="font-size:12pt;background-color:white;"
id="divtagdefaultwrapper">
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><br>
</span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><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" size="1"
color="#500050"><span
style="font-size:12.79px;"><br>
</span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><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" size="1"
color="#222222"><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" size="1"
color="#500050"><span
style="font-size:12.79px;"><br>
</span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><br>
</span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><font
color="black">Thank you</font></span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><br>
</span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><font
color="black">Best regards,</font></span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><br>
</span></font></div>
<div><font face="Arial,sans-serif" size="1"
color="#500050"><span
style="font-size:12.79px;"><font
color="black">Stefano</font></span></font></div>
</span></font></div>
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