********> bugfix.41 Correction Author: David A. Pearlman Correction Date: 5/11/92 Programs: GIBBS Severity: slight Problem: This "bugfix" report improves a few points of minor confusion in the GIBBS manual. Affects: N/A Cause: N/A Fix: Make the following changes to the gibbs manual ---To file doc/gibbs.me ----------------------------------------------------- ---- old lines: 10.1 NTF Flag for force evaluation. Typically set to the same value as NTC (line 9). = 1 complete interaction is calculated = 2 bond interactions involving H-atoms omitted (use with NTC = 2, see above SHAKE options) ---- new lines: 10.1 NTF Flag for force evaluation. Typically set to the same value as NTC (line 9). = 1 complete interaction is calculated = 2 bond interactions involving H-atoms omitted, except bonds in the perturbed group (use with NTC = 2, see above SHAKE options) ---To file doc/gibbs.me ----------------------------------------------------- ---- old lines: 12.10 ISANDE Flag to output enthalpies and entropies, as well as free energies. Note that these quantities are typically an order of magnitude or more less precise than free energy values, and will be much more sensitive than free energies to the completeness of the ensemble statistics collected. See the discussion following the input description for more information. ---- new lines: 12.10 ISANDE Flag to output enthalpies and entropies, as well as free energies. Note that these quantities are typically an order of magnitude or more less precise than free energy values, and will be much more sensitive than free energies to the completeness of the ensemble statistics collected. See the discussion following the input description for more information. Setting ISANDE = 1 will also force the printing of the integrand quantity $< partial V / partial lambda >$\fC when Thermodynamic Integration is being performed (see the IDIFRG flag, 14.6). This can be useful if the user wishes to apply an alternative integration algorithm. ---To file doc/gibbs.me ----------------------------------------------------- ---- old lines: In addition to the integrated free energy, the value of $< partial V / partial lambda >$ \fCwill be output at every energy update, so a different integration algorithm can be applied by the user, if desired. ---- new lines: In addition to the integrated free energy, if ISANDE is set = 1 (see flag 12.10), the value of $< partial V / partial lambda >$ \fCwill be output at every energy update, so a different integration algorithm can be applied by the user, if desired. ---To file doc/gibbs.me ----------------------------------------------------- ---- old lines: 15.1 NSTEPE The number of steps of Equilibration before collecting the Free Energy Statistics. For each window the system is equilibrated for NSTEPE steps. (When ISDYN=\(+-3, NSTMEQ serves the same purpose). 15.2 NSTEPA The number of steps for data collection. The averaging is performed over this number of steps. (When ISLDYN=\(+-3, NSTMUL serves the same purpose). ---- new lines: 15.1 NSTEPE The number of steps of Equilibration before collecting the Free Energy Statistics. For each window the system is equilibrated for NSTEPE steps. (When ISDYN=\(+-2 or \(+-3, NSTMEQ serves the same purpose). 15.2 NSTEPA The number of steps for data collection. The averaging is performed over this number of steps. (When ISLDYN=\(+-2 or \(+-3, NSTMUL serves the same purpose). ---To file doc/gibbs.me ----------------------------------------------------- A global substitution with NSTPA replacing NSTEPA should be made. A global substitution with NSTPE replacing NSTEPE should be made. ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Temporary workarounds: N/A. Files affected: GIBBS Documentation file ...amber4/doc/gibbs.me