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From: Chris Moth <chris.moth.vanderbilt.edu>

Date: Thu, 7 Jul 2005 16:50:24 -0500

Here is the source code where the Volume of the bounding cube is multipled by

0.7698004 in tools.c:

dVolume = dMaxX * dMaxY * dMaxZ;

if ( bOct ) (Yes in this case)

dVolume *= 0.7698004; /* = sqrt(1 - 3*cost^2 - 2*cost^3),

where cost = -1/3 = cos(109.471) */

VP0(( " Volume: %5.3lf A^3 %s\n", dVolume, (bOct ? "(oct)" : "") ));

http://www.gromacs.org/documentation/reference_3.2/online/editconf.html

asserts this constant (.77) as well....

I don't have a quick reference on the trigonometry, unfortunately.

Quoting "Lwin, ThuZar" <ThuZar.Lwin.stjude.org>:

*> Dear Amber Users,
*

*>
*

*> I am trying figure out how the volume of the truncated octahedron box is
*

*> calculated. tleap printed out the following information:
*

*> Scaling up box by a factor of 1.222563 to meet diagonal cut criterion
*

*> Solute vdw bounding box: 49.588 45.810 35.593
*

*> Total bounding box for atom centers: 78.930 78.930 78.930
*

*> (box expansion for 'iso' is 27.7%)
*

*> Solvent unit box: 18.774 18.774 18.774
*

*> Volume: 255327.326 A^3 (oct)
*

*> Total mass 134124.640 amu, Density 0.872 g/cc
*

*> Added 6433 residues.
*

*>
*

*> The box information at the end of the restart file (produced from tleap) is
*

*> 69.2212952 69.2212952 69.2212952 109.4712190 109.4712190 109.4712190
*

*>
*

*> Using 69.2212952 as the length of one side of the truncated octahedron and
*

*> using the formula:
*

*> (a^3)*8*(sqrt(2)), the volume I got is 3752529.786 A^3 which is significantly
*

*> higher than 255327.326 A^3 tleap printed out. Can someone help me with how
*

*> volume of truncated octahedron is calculated?
*

*>
*

*> Thank you very much,
*

*> ThuZar
*

*>
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
*

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*

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*

*>
*

-----------------------------------------------------------------

Chris Moth

Vanderbilt University

Email: christopher.moth.Vanderbilt.Edu

-----------------------------------------------------------------------

The AMBER Mail Reflector

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Received on Thu Jul 07 2005 - 23:53:00 PDT

Date: Thu, 7 Jul 2005 16:50:24 -0500

Here is the source code where the Volume of the bounding cube is multipled by

0.7698004 in tools.c:

dVolume = dMaxX * dMaxY * dMaxZ;

if ( bOct ) (Yes in this case)

dVolume *= 0.7698004; /* = sqrt(1 - 3*cost^2 - 2*cost^3),

where cost = -1/3 = cos(109.471) */

VP0(( " Volume: %5.3lf A^3 %s\n", dVolume, (bOct ? "(oct)" : "") ));

http://www.gromacs.org/documentation/reference_3.2/online/editconf.html

asserts this constant (.77) as well....

I don't have a quick reference on the trigonometry, unfortunately.

Quoting "Lwin, ThuZar" <ThuZar.Lwin.stjude.org>:

-----------------------------------------------------------------

Chris Moth

Vanderbilt University

Email: christopher.moth.Vanderbilt.Edu

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Jul 07 2005 - 23:53:00 PDT

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