AMBER Archive (2007)

Subject: AMBER: Dipolar and Inertia Moments

From: kepa koldo burusco (kepaquestions_at_yahoo.es)
Date: Thu Mar 15 2007 - 05:46:17 CST

[15-III-2007]

Hello Amber users,

I have 2 small doubts and maybe someone could help me
a little...

I have run a MD calculations for a set of molecules in
vacuum. Now I would like to calculate the dipolar
moment and also the inertia moments from the
trajectory.

I succesfully did it with ptraj (amber 7 version, the
one we use here), but the output files are a bit weird
for me (especially the ones for the inertia axis...).

The output format for both calculations are, as you
probably know, 10 columns: first one is the snapshot
number, the next 3 ones are the XYZ coordinates for
the vector, the next 3 ones are the XYZ coordinates
for the center of mass, and the last 3 ones are the
XYZ coordinates of the vector framed into the center
of mass system of coordinates.

That seems to be OK for the dipolar moment (I am only
interested in the module of the vector). But I don't
really understand what's going on with the inertia
moments. I mean, I am getting 3 output files (one for
each coordinate X, Y and Z) having also 10 columns...

I mean, I am interested in getting the 3 Moments of
Inertia (for calculating esphericity) but I think that
ptraj is calculating the 3 eigenvectors instead...

Am i right? Does anyone know whether it is possible to
get the 3 eigenvalues using ptraj? If yes... which
version of ptraj?

I'm attaching the input file for ptraj and the 3
output files just to make it clearer for you.

Thank you very much in advance!!!

Kepa K. Burusco

**********************************
PhD Student
Universidad Autonoma de Barcelona
**********************************

                
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