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On 9/09/2011 4:12 AM, Conrado Pedebos wrote:
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cite="mid:1315505559.2834.YahooMailNeo@web46209.mail.sp1.yahoo.com"
type="cite">
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<div style="margin-bottom: 0in;">Dear gmx-users,</div>
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<div style="margin-bottom: 0in;">I am working with a system
composed by
20 molecules which are aggregated in water. I want to
calculate the
dimensions of this aggregate, but it has an elipsoidal
shape, instead
of a globular shape, as follows in this representation: </div>
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<div style="margin-bottom: 0in;"> |</div>
<div style="margin-bottom: 0in;"> _____|______</div>
<div style="margin-bottom: 0in;"> -----( ____________)------X</div>
<div style="margin-bottom: 0in;"> |</div>
<div style="margin-bottom: 0in;"> |</div>
<div style="margin-bottom: 0in;"> Y</div>
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<div style="margin-bottom: 0in;">Which gromacs tool could I
use to
perform this analysis and calculate X and Y (nm) as a
function of
time? </div>
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<br>
I don't think there is anything to do X, but g_mindist -max can do
Y. Aligning your principal axes with the coordinate axes and looking
at the distribution of the coordinates found with g_traj and then
g_analyze is probably the best you can do.<br>
<br>
Mark<br>
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