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From: Giovanni Pavan <giovanni.pavan.supsi.ch>

Date: Wed, 26 Oct 2011 13:35:59 +0200

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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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Oct 26 2011 - 05:00:03 PDT

Date: Wed, 26 Oct 2011 13:35:59 +0200

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Oct 26 2011 - 05:00:03 PDT

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