<div>thank you for the rational explanation. </div>
<div>but is the free energy change in the charge on/off step(~10kJ/mol) small enough to ignore the flucturations? The free energy change in the LJ mutation step is about 8kJ/mol. <br><br></div>
<div class="gmail_quote">On Fri, Jan 16, 2009 at 11:56 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jhub@gwdg.de">jhub@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">friendli wrote:<br>> Dear all,<br>><br>> When I performing mutation free energy calculation from Leu to Ala, I<br>> first turn off the charge on the side chain of Leu. As I read from the<br>
> GMX archive, the dG/dl curve should be rather smooth for turning off the<br>> partial charge.<br>> In this step(charge off/on), however, I can not obtain the expected<br>> smooth dGdl curve.(see the attachment). I did not use soft-core in this<br>
> step.<br>> Is this normal because the mutation is relatively large? If not, what<br>> could be the problem?<br><br></div>The partial charges of the sidechaines of apolar AA (such as Leu) are<br>almost zero, that's why your dGdl is almost zero. Only because of the<br>
small dgdl your curve looks non-smooth, but that's just a scale issue here.<br><br>Best,<br>Jochen<br>
<div>
<div></div>
<div class="Wj3C7c"><br>><br>><br>> the following is part of the topology file.<br>><br>> 17 opls_238 2 LEU N 7 -0.5 14.0067 ;<br>> qtot 0.5<br>> 18 opls_241 2 LEU H 7 0.3 1.008 ;<br>
> qtot 0.8<br>> 19 opls_224B 2 LEU CA 7 0.14 12.011 ;<br>> qtot 0.94<br>> 20 opls_140 2 LEU HA 7 0.06 1.008 ;<br>> qtot 1<br>> 21 opls_136 2 LEU CB 8 -0.12 12.011<br>
> opls_136 0 12.011 ; qtot 0.88<br>> 22 opls_140 2 LEU HB1 8 0.06 1.008<br>> opls_140 0 1.008 ; qtot 0.94<br>> 23 opls_140 2 LEU HB2 8 0.06 1.008<br>
> opls_140 0 1.008 ; qtot 1<br>> 24 opls_137 2 LEU CG 9 -0.06 12.011<br>> opls_137 0 12.011 ; qtot 0.94<br>> 25 opls_140 2 LEU HG 9 0.06 1.008<br>
> opls_140 0 1.008 ; qtot 1<br>> 26 opls_135 2 LEU CD1 10 -0.18 12.011<br>> opls_135 0 12.011 ; qtot 0.82<br>> 27 opls_140 2 LEU HD11 10 0.06 1.008<br>
> opls_140 0 1.008 ; qtot 0.88<br>> 28 opls_140 2 LEU HD12 10 0.06 1.008<br>> opls_140 0 1.008 ; qtot 0.94<br>> 29 opls_140 2 LEU HD13 10 0.06 1.008<br>
> opls_140 0 1.008 ; qtot 1<br>> 30 opls_135 2 LEU CD2 11 -0.18 12.011<br>> opls_135 0 12.011 ; qtot 0.82<br>> 31 opls_140 2 LEU HD21 11 0.06 1.008<br>
> opls_140 0 1.008 ; qtot 0.88<br>> 32 opls_140 2 LEU HD22 11 0.06 1.008<br>> opls_140 0 1.008 ; qtot 0.94<br>> 33 opls_140 2 LEU HD23 11 0.06 1.008<br>
> opls_140 0 1.008 ; qtot 1<br>> 34 opls_235 2 LEU C 12 0.5 12.011 ;<br>> qtot 1.5<br>> 35 opls_236 2 LEU O 12 -0.5 15.9994 ;<br>> qtot 1<br>
><br>> thank you<br>><br>> Qiang<br>><br>><br>><br>><br></div></div>> ------------------------------------------------------------------------<br>><br>><br>> ------------------------------------------------------------------------<br>
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Max Planck Institute for Biophysical Chemistry<br>Computational biomolecular dynamics group<br>Am Fassberg 11<br>D-37077 Goettingen, Germany<br>Email: jhub[at]<a href="http://gwdg.de/" target="_blank">gwdg.de</a><br>Tel.: +49 (0)551 201-2312<br>
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