> I would like to run simulations on ssDNA under 10 mM, 100 mM, 500 mM and 1 M NaCl concentrations by adding the necessary number of Na+ and Cl- ions. Is there any way of specifying this so that the number of ions are calculated automatically? Something similar exists in GROMACS:
> for 100 mM:
> gmxgenion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA -nname CL -neutral-conc 0.1
>
> I checked addIons, addIons2 and addIonsRand, I searched the mailing list, but I do not see this feature.
No, you have to figure out how much you need by hand noting that standard
LEaP built water boxes will shrink a little unless one is clever in
building it (by altering closeness in the solvate commands)... I have an
old Perl script that I use (appended) to figure out how many ions I need.
Also note that many of the AMBER force fields do not necessarily well
represent single strands (either metastable duplex like structure on short
timescales like ~500ns-1 microsecond or over-compacted on longer
timescales). This was a focus effort for force field improvement with the
DE Shaw nucleic acid force field(s).
Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1346-E1355.
doi: 10.1073/pnas.1713027115.
"RNA force field with accuracy comparable to state-of-the-art protein
force fields." Tan D, Piana S, Dirks RM, Shaw DE.
Also, for assessing needed DNA salt concentration, there is a recent
article by Smith and co-workers:
https://pubs.acs.org/doi/10.1021/acs.jctc.7b01254
--tec3
Perl:
% more ~/perl/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);
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Received on Thu Jul 05 2018 - 17:00:03 PDT
