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<p>On Wednesday 30 July 2008 12:58, David van der Spoel wrote:</p>
<p><span style="color:#008000">> Peyman Yamin wrote:</span></p>
<p><span style="color:#007000">> > Hello List!</span></p>
<p><span style="color:#007000">> ></span></p>
<p><span style="color:#007000">> > I use g_sas to calculate the solvent accessible surface area of some</span></p>
<p><span style="color:#007000">> > amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if</span></p>
<p><span style="color:#007000">> > the hydrophilic part is somehow not recognized, or these terms mean</span></p>
<p><span style="color:#007000">> > different things in g_sas context? For Triton, for instance, a big</span></p>
<p><span style="color:#007000">> > surface is hydrophilic, to my knowledge!</span></p>
<p><span style="color:#008000">></span></p>
<p><span style="color:#008000">> xmgrace -nxy sas.xvg</span></p>
<p></p>
<p>Thanks David, but what about other question marks?!</p>
<p></p>
<p>What is hydrophilic area? is it the wetted or solvated or maybe area on which the solvent molecules are with less than a distance apart from surface, or something else? In Triton, the length of the part which is interacting in a hydrophilic way is bigger actually, but I see a result of g_sas telling me that hydrophobic area is ~50 times bigger!!</p>
<p></p>
<p></p>
<p> I use ffG43a1. Is it a strange behavior to calculate SAS from a UA</p>
<p> trajectory?</p>
<p> I mean is the CHx groups' H size taken intro account ?</p>
<p> </p>
<p><span style="color:#007000">> ></span></p>
<p> How is the DGsolv calculated by g_sas? and the areas ? which algorithm?</p>
<p> where is the code? reference?</p>
<p> </p>
<p><span style="color:#007000">> ></span></p>
<p> Is there any program with which one could calculate the volume enclosed</p>
<p> by SAS resulted from g_sas? Just if one used such and can trust any code</p>
<p> available anywhere??</p>
<p></p>
<p> I see different posts in the mailing list addressing the accuracy of</p>
<p> g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?</p>
<p><span style="color:#007000">> ></span></p>
<p> Any comment is truthfully appreciated :)</p>
<p><span style="color:#007000">> ></span></p>
<p> Peyman</p>
<p><span style="color:#007000">> ></span></p>
<p><span style="color:#007000">> ></span></p>
<p><span style="color:#008000"> > P.S. Edmund Husserl believed, that we would indeed be in a nasty</span></p>
<p><span style="color:#008000"> > position, if empirical science were the only kind of science possible.</span></p>
<p></p>
<p>-- </p>
<p>Peyman Yamin</p>
<p>Lehrstuhl fuer Thermische Verfahrenstechnik</p>
<p>Universitaet Erlangen-Nuernberg</p>
<p>Egerlandstr. 3</p>
<p>91058 Erlangen</p>
<p>Phone: +49(0) - 9131 - 85 27671</p>
<p>Mailto: peyman.yamin@cbi.uni-erlangen.de</p>
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