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<p class="MsoNormal" style="line-height: 150%;"><span style="font-family: "Times New Roman","serif";">Hi,</span></p><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5Cinter%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5Cinter%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5Cinter%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"><style>
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<p class="MsoNormal" style="line-height: 150%;"><span style="font-family: "Times New Roman","serif";">I
want to calculate the solvation free energy of Wild-type human IAPP (hIAPP) with
37 residues in length that residu26 isoleucine is mutated to proline (ile26pro).
I used dual topology in Thermodynamic integration (TI) for calculating salvation
free energy. <span style=""> </span>For the solvation free
energy calculations I need some parameter as <b>Sc_alpha</b>, <b>Sc_power</b>
and <b>Sc_power </b>in<b> </b>mdp file. </span></p>
<p class="MsoNormal" style="line-height: 150%;"><span style="font-family: "Times New Roman","serif";">I
also read manual of Dr David van der spoel about salvation free energy and
manual of Gromacs. Nevertheless, I couldn’t decide best value for these parameters
and my protein.</span> <span style="font-family: "Times New Roman","serif";"></span></p>
<p class="MsoNormal" style="line-height: 150%;"><span style="font-family: "Times New Roman","serif";">I
used the following values in mdp file:</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";">free_energy<span style=""> </span>= yes</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";">init_lambda<span style=""> </span>= 0.00</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";">sc_alpha<span style=""> </span>= 0.5</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";">sc_power<span style=""> </span>= 1.0</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";">sc_sigma<span style=""> </span>= 0.3</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<p class="MsoNormal" style="line-height: 150%;"><span style="font-family: "Times New Roman","serif";">What
values do you suggest for these parameters?</span></p>
<span style="font-family: "Times New Roman","serif";"></span>
<br>Thanks very much,<br>Afsaneh Maleki<br><br>