Adventures in Computational Chemistry

Returning to xleap again. The box I require this time has little tricky requirements. 1) The box should satisfy the molarity ratio for the solute: solvent. 2) Should be big enough that QMMM calculations can be carried out easily 3) combine sets of molecule-pairs which are interconvertible following a proton transfer. I have a pair of molecules say p(H)--i which can be converted to another set called P--I(H) following a proton transfer from p to i.So, p(H)--i <---> P-I(H) To fulfill condition (1), I initially created one molar box for p(H)--i called "PIN" and other box for P--I(H) called "PII" For condition (2) and (3), I created a bigger box with 7 PIN and 1 PII boxes. The idea is: after proton transfer from I to P, during the QMMM calculation, P--I(H) pair coming from "PII" should convert to p(H)--i pair like other pairs from "PIN" and the whole box should become homogeneous with 8 p(H)--i pairs. We begin with: PIN with ...

GNUPLOT can be used to generate histograms. The script below allows one to plot variations in angle from 0° to 180°. Each histogram box width correspond to 3° (covered here under bw option). To execute this script; type this in the terminal: gnuplot histogram.p You should be in the folder where below script is saved in a file name "histogram.p" and a dat file (here, it is N---H-O.dat) should be present. histogram.p ------------------ set term gif set output "angle_N---H-O.gif" set xrange [0.0:180.0] set boxwidth 2.0 absolute set style fill solid 1.0 border -1 set xtics 10 set title "molecule 3.0A Angle N---H-O" set ylabel "occurance" set xlabel "angle" bw = 3   # substitute what you want bin(x,width)=width*floor(x/width) plot 'N---H-O.dat' using (bin($2,bw)):(1.0) smooth freq with boxes ------------------ The dat file is an input file with data in the format: 0    23.680344 1    73.766251 2    67.4...