[gmx-users] regarding rmsd and gyrate

[priya thiyagarajan]

hello sir ,

i got few basic doubts in dynamics..

while performing analysis, we are calculating rmsd and gyrate  for single
molecule..

but in case of more molecules i.e by adding 20 molecules randomly using
genbox , when we perform analysis, rmsd value we are obtaining is the
average change in structure deviation from initial structure.

what about gyrate??

i am getting one plot... how to interpret the result for 20 moecules..since
20 molecules arranged randomly, how it calculates the gyrate value..

please help me with your answer..
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