[gmx-users] g_gyrate options

Juliette N. joojoojooon at gmail.com
Tue Mar 29 18:51:22 CEST 2011

Hi everyone,

I have a question about -nmol option of g_gyrate -h :

With the -nmol option the radius of gyration will be calculated for multiple
molecules by splitting the analysis group in equally sized parts.

If there are 4 chains ABCD in the solvent, and each chain has n atoms of
different types numbered as :  A_1 to A_n, B_n+1 to B_2n, C_2n+1 to C_3n and
D_3n+1 to D-4n.. defining all these atoms in group [4 polymer chain atoms]
together with -nmol option of g_gyrate gives average Rg of each chain? Is
the program really able to tell 4 chains apart and what it reports is wrt
center of mass of each chain? or it takes all atoms of [4 polymer chain
atoms] and computes a new center of mass for the union of all chains..!?

>From -nmol option I got 1.4 nm but averaging over each chain separately
gives 1.9 nm which I think shows a significant difference.

Can you please also clarify what do principle axis and RgX, RgY...refer to?

and my last question is what -p option of g_polystat gives is wrt to which
axis? principle or the average of RgX, RgY, RgZ?

Many thanks for your help.
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