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On 9/04/2011 1:24 PM, Mu Yuguang (Dr) wrote:
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">Dear Chi-Xheng,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">We have tried GB module in gromacs, but
unfortunately we found something wrong with it.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">What we found is that the results got from
gromacs were quite different from those obtained from AMBER
codes.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31,
73, 125);">We did not check in details why.</span></p>
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<br>
I also have tried to compare some polyalanine implicit-solvation
REMD with published AMBER results. I could not get agreement,
however I noted that in a follow-up paper by the same authors using
a higher AMBER version, they implied that they didn't get agreement
with their earlier work, either. So perhaps there was an AMBER
problem, or an AMBER-user problem. I can supply some details if
useful.<br>
<br>
Mark<br>
<span style="font-size: 11pt; font-family:
"Calibri","sans-serif"; color: rgb(31, 73,
125);"><o:p> </o:p></span>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
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73, 125);"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family:
"Tahoma","sans-serif";">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto: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 class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] Still model<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi all,<o:p></o:p></p>
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<p class="MsoNormal">I looked at source code in
/src/mdlib/genborn.c and have two questions regarding the
Still implicit solvent model.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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.<o:p></o:p></p>
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<p class="MsoNormal">2. in calc_gb_rad_still(), does dccf miss
a factor of 2? ( hope I did my math correct....)<o:p></o:p></p>
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<p class="MsoNormal">Thanks in advance!<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Regard,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Chi-xheng<o:p></o:p></p>
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