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

Date: Thu, 27 Oct 2011 17:44:27 +0200

Thank you David for the explanation.

It makes perfectly sense since I was looking at a

structure created by leap.

Just a quick additional point, maybe it is a naive

question, but...what about the 1st point mentioned in my

original email?

"I need 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."

Thank you very much in advance,

giovanni

On Thu, 27 Oct 2011 08:10:02 -0400

David A Case <case.biomaps.rutgers.edu> wrote:

*> On Wed, Oct 26, 2011, Giovanni Pavan wrote:
*

*>>
*

*>> 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?
*

*>
*

*> If you are looking at an inpcrd file created by LEaP
*

*>(say using the solvateBox
*

*> option), there is a deliberate gap between periodic
*

*>boxes, in order to remove
*

*> bad overlaps. So, visualization might lead you to think
*

*>that the box size is
*

*> smaller than it really is.
*

*>
*

*> This effect should go away after presssure
*

*>equilibration.
*

*>
*

*> If you are looking at an equilibrated inpcrd file, then
*

*>there is probably some
*

*> other explanation.
*

*>
*

*> ....dac
*

*>
*

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Received on Thu Oct 27 2011 - 09:00:03 PDT

Date: Thu, 27 Oct 2011 17:44:27 +0200

Thank you David for the explanation.

It makes perfectly sense since I was looking at a

structure created by leap.

Just a quick additional point, maybe it is a naive

question, but...what about the 1st point mentioned in my

original email?

"I need 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."

Thank you very much in advance,

giovanni

On Thu, 27 Oct 2011 08:10:02 -0400

David A Case <case.biomaps.rutgers.edu> wrote:

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Received on Thu Oct 27 2011 - 09:00:03 PDT

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