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From: Jun Wang <jwang20.uci.edu>

Date: Wed, 19 Sep 2007 12:45:52 -0700 (PDT)

Hello!

I calculated the image distances of two center mass of the specified atoms

in truncated octahedron box by using ptraj. Because ptraj can not

calculate the imaged distance correctly when the non-imaged distance is

greater than two time box size, I implemented the algorithm which GROMOS

use to calculate the image distance in truncated octahedron box. But some

of the imaged distances calculated by this new program are very small (<

1.0 A). I give out the code below and look forward some advices.

...

/*the origin is set at Ri , (X,Y,Z) is the new coordinates of the atom j

X = Xj - Xi

Y = Yj - Yi

Z = Zj - Zi

/*The atom j is moved into the positive quadrant with respect to an origin

at 0*/

if ( X < 0 ) X = -X;

if ( Y < 0 ) Y = -Y;

if ( Z < 0 ) Z = -Z;

while ( X > box[0] ) X = X - box[0];

while ( Y > box[1] ) Y = Y - box[1];

while ( Z > box[2] ) Z = Z - box[2];

/*The atom j is moved into the truncated octahedraon box with respect to

an center at (box[0]/2,box[1]/2,box[2]/2)

if ( fabs(X-box[0]/2.0)+fabs(Y-box[1]/2.0)+fabs(Z-box[2]/2.0) >

0.75*box[0] ) {

X=X-((X-box[0]/2.0>=0)?1:-1)*box[0]/2.0;

Y=Y-((Y-box[1]/2.0>=0)?1:-1)*box[1]/2.0;

Z=Z-((Z-box[2]/2.0>=0)?1:-1)*box[2]/2.0;

}

/*The atom j is moved into the truncated octahedraon box with respect to

an center at the origin)

X=X-box[0]/2.0;

Y=Y-box[1]/2.0;

Z=Z-box[2]/2.0;

return(X*X+Y*Y+Z*Z);

===========================================

Jun Wang, Ph.D.

Dept Molecular Biology & Biochemistry

University of California, Irvine, CA 92697

Phone: (949) 824-9562

Email: jwang20.uci.edu

===========================================

Received on Sun Sep 23 2007 - 06:07:17 PDT

Date: Wed, 19 Sep 2007 12:45:52 -0700 (PDT)

Hello!

I calculated the image distances of two center mass of the specified atoms

in truncated octahedron box by using ptraj. Because ptraj can not

calculate the imaged distance correctly when the non-imaged distance is

greater than two time box size, I implemented the algorithm which GROMOS

use to calculate the image distance in truncated octahedron box. But some

of the imaged distances calculated by this new program are very small (<

1.0 A). I give out the code below and look forward some advices.

...

/*the origin is set at Ri , (X,Y,Z) is the new coordinates of the atom j

X = Xj - Xi

Y = Yj - Yi

Z = Zj - Zi

/*The atom j is moved into the positive quadrant with respect to an origin

at 0*/

if ( X < 0 ) X = -X;

if ( Y < 0 ) Y = -Y;

if ( Z < 0 ) Z = -Z;

while ( X > box[0] ) X = X - box[0];

while ( Y > box[1] ) Y = Y - box[1];

while ( Z > box[2] ) Z = Z - box[2];

/*The atom j is moved into the truncated octahedraon box with respect to

an center at (box[0]/2,box[1]/2,box[2]/2)

if ( fabs(X-box[0]/2.0)+fabs(Y-box[1]/2.0)+fabs(Z-box[2]/2.0) >

0.75*box[0] ) {

X=X-((X-box[0]/2.0>=0)?1:-1)*box[0]/2.0;

Y=Y-((Y-box[1]/2.0>=0)?1:-1)*box[1]/2.0;

Z=Z-((Z-box[2]/2.0>=0)?1:-1)*box[2]/2.0;

}

/*The atom j is moved into the truncated octahedraon box with respect to

an center at the origin)

X=X-box[0]/2.0;

Y=Y-box[1]/2.0;

Z=Z-box[2]/2.0;

return(X*X+Y*Y+Z*Z);

===========================================

Jun Wang, Ph.D.

Dept Molecular Biology & Biochemistry

University of California, Irvine, CA 92697

Phone: (949) 824-9562

Email: jwang20.uci.edu

===========================================

Received on Sun Sep 23 2007 - 06:07:17 PDT

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