AMBER Archive (2009)

Subject: Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Tue Jul 28 2009 - 23:19:41 CDT

Dear Thomas, as I understand this script works only for the cubic box, is there somethng for the octahedral box?

Best regards,
Andrew Voronkov

17.07.09, 20:50, "Thomas Cheatham III" :

> > My first question is related to neutralization procedure.
> ...
> > Let's assume that N1>N2 (overal charge is positive).
> >
> > Here I have two possibilities how to neutralize given system:
> >
> > #1
> > Add just n=N1-N2 Cl- counterions.
> "net-neutralization"
> > #2
> > Add N1 Cl- counterions and N2 Na+ counterions.
> "excess salt"
> The third possibility is no salt (which although unphysical due to the
> overall net-charge works in simulation since the Ewald forces do not
> diverge and then there is also this effective net-neutralizing plasma; in
> the past AMBER had two options whereby you could smear out the excess
> charge or use the implicit plasma).
> In 1998, with DNA, I did simulations on a ns time scale and saw little
> difference with each scheme. However, recent posts to the reflector
> pointed out some anomalies with RNA equilibration where it extended
> drastically if no salt was added... I am able to reproduce this and
> recommend you do either #1 or #2. Generally I personally try to match
> experiment so I try to find an added salt concentration close to
> experimental conditions (usually ~200 mM).
> The argument for not adding excess salt with polyanions like nucleic
> acids relates to sampling (since you would have to better sample the
> ionic distribution) and force field parameters (which were flawed and
> led to artificial crystallization)... However, as RNA can bind anions,
> it is probably wise to have Cl- around too. Therefore I would vote for
> #2.
>
> > My second question is related to ionic strength (IS).
> Ionic strength is complicated since you have the solute charges and also
> ion charges that contribute. The way I logically get around this is to
> specify that I add net-neutralizing salt to balance the overall charge and
> then add a certain concentration of excess salt (like 200 mM). The
> overall ionic strength should include all charges; however you could also
> report the ionic strength of the added salt.
> > the reference volume (for calculation of NaCl concentration) is the overal
> > volume of water molecules as it is reported here:
> >
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3943.html
> I have a perl script that I plug in the box size and molarity I want and
> it, based on volume (**not correcting for the volume of solute**), tells
> me how many ions to add. Remember also that by default LEaP produces
> water boxes that are slightly less dense than expected. I append the perl
> script below.
> --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);
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber