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<div id="divtagdefaultwrapper" style="background-color:white;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt;background-color:white;" id="divtagdefaultwrapper"></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;" id="divtagdefaultwrapper">
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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>
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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>
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<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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