Thank you for the suggestion. I will have a try.
Best,
Ren
-----Original Message-----
From: Aron Broom [mailto:broomsday.gmail.com]
Sent: Wednesday, August 08, 2012 2:28 PM
To: AMBER Mailing List
Subject: Re: [AMBER] how to make a certain ionic concentration for the system?
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
> America's "Best Hospitals" in 13 specialties. Named to FORTUNE(r) Magazine's
> "100 Best Companies to Work For(r)" list seven years in a row. Designated as
> a Magnet hospital for excellence in nursing. Visit us at
> methodisthealth.com. Follow us at twitter.com/MethodistHosp and
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list seven years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at methodisthealth.com. Follow us at twitter.com/MethodistHosp and www.facebook.com/MethodistHospital.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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Received on Thu Aug 09 2012 - 10:00:04 PDT
