ensemble-dg / ensemble-dg-same

Table of Contents

Name

ensemble-dg, ensemble-dg-same - compute free energy of an ensemble of species

Synopsis

ensemble-dg [OPTION]... PREFIX1 PREFIX2
ensemble-dg-same [OPTION]... PREFIX

Description

ensemble-dg computes the free energy fo a two-sequence ensemble. The input to ensemble-dg consists of the outputs of running hybrid or hybrid-ss on each species, as well as the output of running concentration on the ensemble. ensemble-dg writes PREFIX1-PREFIX2.ens.dG which containts the partition function and free energy of the ensemble at each temperature.

ensemble-dg-same operates in the same manner on a one-sequence ensemble, using the output from concentration-same.

It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl and ensemble-dg and ensemble-ext instead of running ensemble-dg directly.

Options

-x, --exclude=A|B|AA|BB
excludes the specified species from consideration. May be used more than once, to exclude multiple species.
-H, --enthalpy=value
assigns value kcal/mol of enthalpy to stacking in single strands, in proportion to the lengths of the sequences. Must be used with --entropy.
-S, --entropy=value
assigns value cal/mol/K of entropy to stacking in single strands, in proportion to the lengths of the sequences. Must be used with --enthalpy.
-o, --output=prefix
names output files with prefix.
-Y, --infinity
enables "infinite temperature correction": the partition functions for each species are corrected according to values in A.inf, B.inf, A-A.inf, B-B.inf and A-B.inf.

Table of Contents