lammps lammps wrote:
Not R_x, R_y, and R_z.
What I want to obtain are the three three principal moments of the
ellipsoidal macromolecule.
They are different quantities.
Then isn't g_principal the more appropriate tool, rather than g_gyrate?
-Justin
2011/5/10 Erik Marklund <er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se>>
Mark Abraham skrev 2011-05-10 12.31:
On 10/05/2011 8:23 PM, lammps lammps wrote:
Hi,
I want to study the shape change of a macromolecule which
seems like a ellipsoid. So, I need obtain the three
principal moments of the molecules.
Is the command of g_gyrate helpful for me? The sum of the
three principal moments should be equal to the <Rg^2>.
However, I used the command g_gyrate -f traj.gro -s nvt.tpr
-n anly.ndx -o shape.xvg -p obtain the Rg and other three
qualities.
It seems that the sum of the last three qualities is not
equal to the Rg^2. Is there something wrong?
Why should that sum equal Rg^2?
Mark
Shouldn't it be half of that sum?
Rg^2 = 1/N Sum([r_k - <r>]^2),
where r are vectors and masses are set to unity for conveniance. If
decomposed in orthonormal axes x, y, and z, it yealds
Rg^2 = 1/N Sum([x_k-<x>]^2 + [y_k-<y>]^2 + [z_k-<z>]^2).
The radius of gyration around e.g. the x-axis is
Rg_x^2 = !/N Sum([y_k-<y>]^2 + [z_k-<z_k>]^2).
Hence Rg^2 = (Rg_x^2+Rg_y^2+Rg_z^2) / 2.
That matches the numbers I get from my tests.
--
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se>
http://folding.bmc.uu.se/
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Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
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