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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>OPLS-aa force field is good for beta
structure, it is not so good for alpha helix study.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Amber99f force field is good for alpha
helix , but not good for beta structure<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best regards</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Yuguang</span></font><font color=navy><span
style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dr. Yuguang Mu</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Assistant Professor</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
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color:navy'> Sciences</span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
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size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> <st1:country-region w:st="on"><st1:place w:st="on">Singapore</st1:place></st1:country-region>
637551 Tel: +65-63162885 Fax: +65-67913856</span></font><font color=navy><span
style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
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color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'> </span></font><o:p></o:p></p>
</div>
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<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Navratna Vajpai<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, September 14, 2006
9:50 PM<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Discussion
list for GROMACS users</st1:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users] Hi...</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Sorry for not so explicitly explaining the things.. Here it
goes<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I have a nona peptide and I ran a MD of 20ns using OPLS-AA force
field. <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>when I used the OPLS-AA the phi angles came out to be -ve for three of
the amino acids. which is stericaly not allowed. But when I ran it using
GROMOS I found all the phi-psi combinations with a negative phi value
distribution. But now I am lost as you have said it works only for GROMOS like
force field. Why?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>and if that so I have got -ve phi distribution for the other phi-psi
plots. <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>My other question remained unanswered even now. Is there any way
really to judge which force field is to be chosen for particular type of
analysis?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Best regards <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Thanks<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Sep 14, 2006, at 3:36 PM, David van der Spoel wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Navratna Vajpai wrote:<o:p></o:p></span></font></p>
</div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi all.. I wrote this mail yesterday. But could not receive any reply
till now. So if someone can suggest something about it. That would be nice.
Best regards<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Nav<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Begin forwarded message:<o:p></o:p></span></font></p>
</div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>*From: *Navratna Vajpai <navratna.vajpai@unibas.ch <<a
href="mailto:navratna.vajpai@unibas.ch">mailto:navratna.vajpai@unibas.ch</a>>><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>*Date: *September 13, 2006 10:32:21 AM GMT+02:00<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>*To: *<st1:PersonName w:st="on">Discussion list for GROMACS users</st1:PersonName>
<gmx-users@gromacs.org <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>>><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>*Subject: **[gmx-users] Hi...*<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>*Reply-To: *<st1:PersonName w:st="on">Discussion list for GROMACS users</st1:PersonName>
<gmx-users@gromacs.org <<a href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a>>><o:p></o:p></span></font></p>
</div>
<div style='min-height: 14px'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dear All<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi.. This is in regard to your previously replied mail regarding the
use of GROMOS96 or OPLS-AA or AMBER force field.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>As you said it depends upon the users taste which one to use. This
means that the three on a broad manner should give convergence of the analyzed
data set. Infact from my simulation runs using oplss-aa and gromos96, I didn't
found that. I tried using the GROMOS96 and opls-aa force field on my small
peptides for a period of 20ns and found that with opls-aa even the phi-psi
combination of the individual amino acids were incorrect. Actually this always
puzzled me to make a choice for the Force field.<span
class=apple-converted-space> </span>The rest of the script was unchanged
for the two runs.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Could you please comment on the above results? Is there any way really
to judge which force field is to be chosen for particular type of analysis?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Best regards<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Nav<o:p></o:p></span></font></p>
</div>
<div style='min-height: 14px'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</blockquote>
</blockquote>
<div style='min-height: 14px'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div style='min-height: 14px'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>what do you mean with incorrect? your question is quite vague.<o:p></o:p></span></font></p>
</div>
<div style='min-height: 14px'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>the g_rama program works only for GROMOS like force fields
unfortunately but that doesn't mean the phi/psi are wrong. What would be the
"correct" result anyway? Maybe your peptide unfolds.<o:p></o:p></span></font></p>
</div>
<div style='min-height: 14px'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>--<span class=apple-converted-space> </span><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>David.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>________________________________________________________________________<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dept. of Cell and Molecular Biology, <st1:place w:st="on"><st1:PlaceName
w:st="on">Uppsala</st1:PlaceName> <st1:PlaceType w:st="on">University</st1:PlaceType></st1:place>.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Husargatan 3, <st1:address w:st="on"><st1:Street w:st="on">Box</st1:Street>
596</st1:address>,<span class=apple-converted-space> </span><span
class=apple-tab-span> </span>75124 <st1:place w:st="on"><st1:City
w:st="on">Uppsala</st1:City>, <st1:country-region w:st="on">Sweden</st1:country-region></st1:place><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>phone:<span class=apple-tab-span> </span>46 18 471 4205<span
class=apple-tab-span> </span>fax: 46 18 511 755<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><span
class=apple-tab-span> </span>spoel@gromacs.org <span
class=apple-converted-space> </span>http://folding.bmc.uu.se<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>_______________________________________________<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>gmx-users mailing list<span class=apple-converted-space> </span><a
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><o:p></o:p></span></font></p>
</div>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div><span style='border-spacing: 0px 0px;text-align:auto;-khtml-text-decorations-in-effect: none;
-apple-text-size-adjust: auto;orphans: 2;widows: 2;word-spacing:0px'><span
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<div>
<p class=MsoNormal><span class=apple-style-span><span style='border-spacing: 0px 0px;
text-align:auto;-khtml-text-decorations-in-effect: none;-apple-text-size-adjust: auto;
orphans: 2;widows: 2;word-spacing:0px'><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><span
style='border-spacing: 0px 0px;text-align:auto;-khtml-text-decorations-in-effect: none;
-apple-text-size-adjust: auto;orphans: 2;widows: 2;word-spacing:0px'>*******************************************</span></font></span><font
size=1 color=black face=Helvetica><span style='font-size:9.0pt;font-family:
Helvetica;color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>Navratna
Vajpai</span></font></span><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>Ph.
D student in Prof. Grzesiek's laboratory</span></font></span><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>Department
of Structural Biology</span></font></span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>Biozentrum, <st1:place
w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:PlaceName
w:st="on">Basel</st1:PlaceName></st1:place></span></font></span><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p></o:p></span></font></p>
</div>
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<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>Klingelbergstrasse
70,</span></font></span><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
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<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>CH-4056</span></font></span><font
size=1 color=black face=Helvetica><span style='font-size:9.0pt;font-family:
Helvetica;color:black'><o:p></o:p></span></font></p>
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<p class=MsoNormal><st1:place w:st="on"><st1:City w:st="on"><span
class=apple-style-span><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>Basel</span></font></span></st1:City><span
class=apple-style-span><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>, <st1:country-region
w:st="on">Switzerland</st1:country-region></span></font></span></st1:place><span
class=apple-style-span><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>.</span></font></span><font
size=1 color=black face=Helvetica><span style='font-size:9.0pt;font-family:
Helvetica;color:black'><o:p></o:p></span></font></p>
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<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>Phone-
+41 61 267 2080(O)</span></font></span><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
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<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'>
+41 78 744 0810(M)</span></font></span><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p></o:p></span></font></p>
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style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><span class=apple-style-span><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'><a
href="mailto:navratna.vajpai@unibas.ch">navratna.vajpai@unibas.ch</a></span></font></span><font
size=1 color=black face=Helvetica><span style='font-size:9.0pt;font-family:
Helvetica;color:black'><o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p> </o:p></span></font></p>
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style='font-size:9.0pt;font-family:Helvetica;color:black'><br>
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