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<p class=MsoNormal>Dear all,<o:p></o:p></p>
<p class=MsoNormal>I am trying to calculate diffusion coefficients for a system
of (30) glycine molecules in a box with (1000) water.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>After running:<o:p></o:p></p>
<p class=MsoNormal>g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I get a list of diffusion coefficients – one for each
glycine molecule. I then calculate the average and the stdev:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Average=1.004<o:p></o:p></p>
<p class=MsoNormal>Stdev=0.7661<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>My problem is that the stdev is very great! More than +/- 75%
of the average value.<o:p></o:p></p>
<p class=MsoNormal>Why is that?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Also, what is the reason for the trestart=10 default value?
Shouldn’t it be better to have trestart=1, if my xtc file is saved every
1 ps?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks,<o:p></o:p></p>
<p class=MsoNormal>Soren Enemark<o:p></o:p></p>
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