Hi Yuguang,<div>Thanks for the input. For the AMBER vs GROMACS comparison, what GB model you were using, OBC, HCT, or Still. Also, do you notice any source code questions that I mentioned ? </div><div>Thanks</div><div><br>
</div><div>Regard,</div><div><br></div><div>Chi-cheng</div><div><br><div class="gmail_quote">On Fri, Apr 8, 2011 at 10:24 PM, Mu Yuguang (Dr) <span dir="ltr"><<a href="mailto:YGMu@ntu.edu.sg">YGMu@ntu.edu.sg</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Dear Chi-Xheng,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">We have tried GB module in gromacs, but unfortunately we found something wrong with it.
</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">What we found is that the results got from gromacs were quite different from those obtained from AMBER codes.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">We did not check in details why.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Yuguang</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"> </span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>Chi-cheng Chiu<br>
<b>Sent:</b> Saturday, April 09, 2011 8:33 AM<br>
<b>To:</b> <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] Still model</span></p>
</div><div><div></div><div class="h5">
<p class="MsoNormal"> </p>
<p class="MsoNormal">Hi all,</p>
<div>
<p class="MsoNormal">I looked at source code in /src/mdlib/genborn.c and have two questions regarding the Still implicit solvent model.</p>
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<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">1. in the function calc_gb_chainrule(), only Still model have extra factor of 2 apply on dvda, which I don't know why.</p>
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<div>
<p class="MsoNormal">2. in calc_gb_rad_still(), does dccf miss a factor of 2? ( hope I did my math correct....)</p>
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<p class="MsoNormal">Thanks in advance!</p>
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<div>
<p class="MsoNormal"> </p>
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<p class="MsoNormal">Regard,</p>
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<p class="MsoNormal"> </p>
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<p class="MsoNormal">Chi-xheng</p>
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