Dear AMBER users,
I need an information regarding .inpcrd and .rst files in PBC calculations.
Information about the periodic BOX is listed at in the last row of these
files.
The first 3 numbers identify box dimensions along X, Y and Z. But, what is
the correct meaning of the other 3 numbers which identify the angles?
I mean, angles between what?
By convention in crystallography given a, b & c as the three sides of the
cell, alpha, beta & gamma are the angles perpendicular to the vector.
So, for clarity: alpha is the angle between b & c, beta that between a &c
and gamma that between a and b.
Is it the same in .inpcrd and .rst files?
Do the last 6 numbers in those files mean exactly: X, Y, Z, alpha, beta,
gamma?
It is not clear to me since everywhere I found only that the last 3 numbers
refer to "angles" but no precise information is given about these angles.
This is of particular importance when I try to manipulate these files
(.inpcrd) to transform, for instance, a TIP3PBOX in a triclinic one.
I have a last question. When I visualize my periodic box and I measure from
graphical interface the box dimensions, they are about 10% smaller than
those listed at the bottom of the .inpcrd file. Why this?
I hope to receive any feedback from you as soon as possible.
Bye all
Giovanni
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Received on Wed Oct 26 2011 - 05:00:03 PDT
