those are the values of the periodic cell, where x,y,z are the lengths of
the box, and a,b,c are the angles.
A simpler approach, is to solvate your system, then look in the leap.log
file, or onscreen, and look at the volume of your solvated system that is
output after solvation, then just calculate the number of ions needed
beyond those for neutralization.
~Aron
On Wed, Aug 8, 2012 at 12:29 PM, Kong, Ren <rkong.tmhs.org> wrote:
> Hi Amber users,
>
> I'm trying to add ions to make a certain ionic concentration for my
> system, like 0.15 mol/L KCL.
> And I search in the mail list and find Thomas Cheatham III's script:
>
> --tec3
>
>
> molarity.perl
>
> #!/usr/sbin/perl
>
> $molar = $ARGV[0];
> $box_x = $ARGV[1];
> $box_y = $ARGV[2];
> $box_z = $ARGV[3];
> $box_a = $ARGV[4];
> $box_b = $ARGV[5];
> $box_g = $ARGV[6];
>
>
> if ($box_x == 0) {
> printf("Usage: molarity box-x box-y box-z alpha beta gamma\n");
> die;
> }
>
> if ($box_y == 0) {
> $box_y = $box_x;
> }
>
> if ($box_z == 0) {
> $box_z = $box_x;
> }
>
> if ($box_a == 0) {
> $box_a = 90.0;
> }
>
> if ($box_b == 0) {
> $box_b = $box_a;
> }
>
> if ($box_g == 0) {
> $box_g = $box_a;
> }
>
> $torad = 2 * 3.141592654 / 360.0;
>
> $rad_a = $box_a * $torad;
> $rad_b = $box_b * $torad;
> $rad_g = $box_g * $torad;
>
> $angles = 1 - cos($rad_a)*cos($rad_a) - cos($rad_b)*cos($rad_b) -
> cos($rad_g)*cos($rad_g);
> $angles += 2 * cos($rad_a)*cos($rad_b)*cos($rad_g);
> $angles = sqrt($angles);
>
>
> $volume = $box_x * $box_y * $box_z * $angles;
>
>
> $molecules = 6.022 * $volume * $molar / 10000;
>
> printf(" MOLARITY = %8.3f\n", $molar);
> printf(" Box size = %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", $box_x,
> $box_y, $box_z, $box_a, $box_b, $box_g);
> printf(" Volume = %8.3f\n", $volume);
> printf("\n %8.3f molecules are necessary to make a molarity of %6.2f
> M\n\n", $molecules, $molar);
>
> I'm wondering how to get the x,y,z and alpha, beta, gamma value?
> I reviewed the leap.log files and not sure about what these value are.
>
> Does anyone use this scrip to count the ion number?
>
> Thanks a lot.
>
> Ren Kong Ph.D.
>
> Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Aug 08 2012 - 12:30:02 PDT
