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<DIV dir=ltr align=left><SPAN class=912064522-28042009><FONT face=Arial
color=#0000ff size=2>The issue is you don't have enough statistics to get a
meaningful result. Three ways you can get more, more particles, more time,
or multiply runs.</FONT></SPAN></DIV>
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<P><FONT size=2>Catch ya,<BR><BR>Dr. Dallas Warren<BR>Department of
Pharmaceutical Biology and Pharmacology<BR>Pharmacy and Pharmaceutical Sciences,
Monash University<BR>381 Royal Parade, Parkville VIC
3010<BR>dallas.warren@pharm.monash.edu.au<BR>+61 3 9903
9167<BR>---------------------------------<BR>When the only tool you own is a
hammer, every problem begins to resemble a nail.</FONT> </P>
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<FONT face=Tahoma size=2><B>From:</B> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <B>On Behalf Of </B>Sunil
Thapa<BR><B>Sent:</B> Tuesday, 28 April 2009 5:40 PM<BR><B>To:</B>
gmx-users@gromacs.org<BR><B>Subject:</B> [gmx-users] ffgmx:diffusion of
oxygen<BR></FONT><BR></DIV>
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<DIV>Respectable Experts</DIV>
<DIV>Thank you very much David. Yes the msd curve tries to improve if I
run for 100ns. But my system is very small 1oxygen molecule in 255
molecules of water. I want to calculate the self diffusion coefficient
of oxygen . What I have found that people do such simulations for mostly
not more than 10 ns. I also got to see your paper on <STRONG>dynamic
property of water/alcohol mixture</STRONG> where you have used time less
than 10 ns. Which msd curve is to take ?</DIV>
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<DIV>Another query : I want to simulate the system in a bit higher
temperature 310 K . What are the parameters I should change in
the mdp file. I saw the previous mails about it. Eric says that
only time step should be small in order to constrain the bonds. Are
there any other things?</DIV>
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