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From: Jason Swails <jason.swails.gmail.com>

Date: Mon, 29 Sep 2014 08:06:25 -0400

On Mon, 2014-09-29 at 00:42 -0700, amirhossein taghavi wrote:

*> Hi,
*

*>
*

*> I removed the noimage from script and added the parmbox info plus the
*

*> angles as you said and the problem is solved.Thanks a lot!
*

*> May I ask what do you mean by 'corner case' and how can I learn more
*

*> about the algorithms that cpptraj uses to analyze bonds,dihedrals
*

*> and ....
*

In most cases, either the topology file, the trajectory file, or both

will give cpptraj enough information to determine what the shape of the

unit cell is. Without the shape (i.e., the angles between the unit cell

basis vectors), you have no way of determining the periodic images of

any particle.

It is unusual for files fed to cpptraj to contain _only_ the lengths of

the periodic cells and not the angles. Since this isn't enough

information to perform imaging, cpptraj pretends there is no box (this

is the "corner case"). The algorithm for computing distances and angles

are quite simple -- the same that you learn in basic geometry. When

unit cell vectors are defined, cpptraj will compute distances using the

minimum image convention (i.e., find the image of particle 2 that is

closest to the chosen image of particle 1 and compute that distance).

HTH,

Jason

Date: Mon, 29 Sep 2014 08:06:25 -0400

On Mon, 2014-09-29 at 00:42 -0700, amirhossein taghavi wrote:

In most cases, either the topology file, the trajectory file, or both

will give cpptraj enough information to determine what the shape of the

unit cell is. Without the shape (i.e., the angles between the unit cell

basis vectors), you have no way of determining the periodic images of

any particle.

It is unusual for files fed to cpptraj to contain _only_ the lengths of

the periodic cells and not the angles. Since this isn't enough

information to perform imaging, cpptraj pretends there is no box (this

is the "corner case"). The algorithm for computing distances and angles

are quite simple -- the same that you learn in basic geometry. When

unit cell vectors are defined, cpptraj will compute distances using the

minimum image convention (i.e., find the image of particle 2 that is

closest to the chosen image of particle 1 and compute that distance).

HTH,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Sep 29 2014 - 05:30:03 PDT

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