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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'>Hi,<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The GROMACS user manual is a good place to
start. For more specific help you will probably need to provide details of
exactly what you want to do.<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'>What are you simulating? What are the questions
you are hoping to answer? <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>
<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best wishes,<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>-Syma<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 style='margin-bottom:12.0pt'><font size=2 color=navy face="Times New Roman"><span
style='font-size:10.0pt;color:navy'>********************************************************************<br>
<br>
Dr. Syma
Khalid
e-mail: <u1:PersonName u2:st="on">syma.khalid@bioch.ox.ac.uk</u1:PersonName><br>
Dept. of
Biochemistry
phone: (0)1865-275380<br>
<u1:place u2:st="on"><u1:PlaceType u2:st="on"><st1:place w:st="on"><st1:PlaceType
w:st="on">University</u1:PlaceType></st1:PlaceType> of <u1:PlaceName u2:st="on"><st1:PlaceName
w:st="on">Oxford</u1:PlaceName></u1:place></st1:PlaceName></st1:place>
fax: (0)1865-275273<br>
<u1:address u2:st="on"><u1:Street u2:st="on"><st1:address w:st="on"><st1:Street
w:st="on">South Parks Road</u1:Street></st1:Street> <br>
<u1:City u2:st="on"><st1:City w:st="on">Oxford</u1:City></u1:address></st1:City></st1:address><br>
OX1 3QU<br>
<u1:place u2:st="on"><u1:country-region u2:st="on"><st1:country-region w:st="on"><st1:place
w:st="on">U.K.</u1:country-region></u1:place></st1:place></st1:country-region><br>
________________________________</span></font><o:p></o:p></p>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span lang=EN-US 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 lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span lang=EN-US 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>Alif M Latif<br>
<b><span style='font-weight:bold'>Sent:</span></b> 29 August 2007 19:19<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Self-assembly
lipid simulation</span></font><span lang=EN-US><o:p></o:p></span></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>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dear Gromacs users,<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'>I'm doing MD Simulation on self-assembly of lipid molecules using
gromacs. If someone can kindly help me find the conditions (for my .mdp file)
for these kind of simulation? There are many choices and i would like to ask
for opinion on general (usually) conditions used in the .mdp file for the
simulation. I would like to look for physical and some thermodynamical
properties from my simulation results. This is to aid the experimental results
done. <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'>Any paper or links also can help me a lot. I have read many papers but
i thought maybe u guys can help add more to it. This is because not much
options i can find in those papers and not all of them use gromacs.Thanks for
reading and your help is greatly appreciated. Thanks again.<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'> <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'>M. Alif M. Latif<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'>Chemistry Department, Faculty of Science,<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'>Universiti Putra <st1:country-region w:st="on"><st1:place w:st="on">Malaysia</st1:place></st1:country-region>,<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'>43400 UPM Serdang, Selangor,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><st1:country-region w:st="on"><st1:place w:st="on"><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Malaysia</span></font></st1:place></st1:country-region><o:p></o:p></p>
</div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=1 width="100%" align=center>
</span></font></div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Take the Internet to Go: Yahoo!Go puts the <a
href="http://us.rd.yahoo.com/evt=48253/*http:/mobile.yahoo.com/go?refer=1GNXIC">Internet
in your pocket:</a> mail, news, photos & more. <o:p></o:p></span></font></p>
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