NONEQ4.EXE : (Version 1.142, 29 May, 1994 for PC)
This program generates concentration distributions for the model
of a reversibly associating non-ideal system.
The program starts by asking for a choice between input of positions
in terms of r (radius) or of XI (= r^2/2).
An output filename is then requested. The same file-name can be reused without
loss of data since the files are always appended to.
Parameter Input Menu:
Before starting calculations the necessary parameters are requested.
In all cases, the default (or previous) values may be accepted by entering
a and the valid range of the parameters is indicated.
The requested parameters are:
Meniscus position, in either in units of XI ( r^2/2) [cm^2] or in r [cm].
Base position, in either in units of XI ( r^2/2) [cm^2] or in r [cm].
Cutoff gradient, in units of 1/(cm^2/2), represents the maximum
gradient for which to write usable output data. This can be used to
exclude unrealistic concentration distributions.
Number of (original, i.e. before cutoff) data points to calculate.
Initial total loading concentration for the simulation, in units
proportional to the weight concentration, typically in fringes or
in absorbance.
Monomer value of sigma = w^2 * M(1-Vp)/RT for the monomer.
Number of monomer - n:mer equilibria to use followed by paired values of:
Degree of association, i.e. n of the n:mer; (this value can be
nonintegral for pressure dependent systems).
and
Association constant in units of (the weight concentration used )^(1-n)
for each of the monomer - n:mer equilibria to be used.
Second Virial Coefficient in units of (the weight concentration used )^(-1)
The calculations are then performed. A measure of reliability of the resulting
concentration distributions is given by integrating the mass present in the
data channel and thus estimating the initial loading concentration. This mass
is then compared to the mass directly obtained from the actual initial
loading concentration parameter used in the calculations. Warning messages
are issued for significant discrepancies between these values. These
messages are needed only for severely nonideal or extremely associated
systems. Other checks, especially for overflow problems, are also performed.
The main menu is presented after performing the calculations.
Main Menu:
This menu requests the next action of the program. The options are:
D: (done) write concentrations as a function of position to the
preselected output file.
G: select a graphical menu to choose the form of the presentations
of the calculated distibutions and derived parameters.
N: (noise) perturb already calculated total concentration
distributions by adding random noise to otherwise "perfect"
data, and then write the data to the current output file.
[Note that repeated applications of noise to the data are
NOT cumulative.]
S: set [ or U: for unset] a flag to write out the individual concentrations
of (up to) the first 11 oligomers used in the calculations.
I: integrate c*d(XI) to provide a measure of the total mass in the distribution.
Q: exit the program WITHOUT writing an output file.
NO ENTRY (i.e. ): start a new calculation.
The Graphical Output Menu provides the following options
1 - TOTAL - concentration vs. POSITION
2 SPECIES concentration vs. POSITION
3 LN(species concentration) vs. POSITION
4 SPECIES Weight FRACTION vs. POSITION
5 LN(species weight fraction) vs. POSITION
6 SPECIES concentration vs. TOTAL concentration
7 LN(species concentration) vs. TOTAL concentration
8 SPECIES Weight FRACTION vs. TOTAL concentration
9 SIGMAS vs. POSITION
10 SIGMAS vs. CONCENTRATION
11 GRADIENT of total concentration vs. POSITION
12 GRADIENT of total conc vs. TOTAL concentration
13 RETURN to main part of program
It should be noted that only the first of these plotting options is available
after modulating the data with noise.]