MigrationGuide0102

Migration guide from ver. 0.1 to 0.2

The following points are different from ver. 0.1:

• Directory name is now ermod-0.2.x instead of enerepr-0.1.x
• ermod_namd and ermod_gromacs is merged into a single file, ermod.
• Users for NAMD version should also set ERMOD_PLUGINS environment variable.
  • If you install program by make install you don't have to do anythiing. This is the recommended usage.
  • If not, set environment variable every time before you run the program. In the below the extracted directory is assumed to be /path/to/ermod-0.2.x.
    • For sh/bash/zsh, export ERMOD_PLUGINS=/path/to/ermod-0.2.x/vmdplugins/libexec
    • For csh/tcsh, setenv ERMOD_PLUGINS /path/to/ermod-0.2.x/vmdplugins/libexec
• Users for GROMACS version should run new version of gen_structure and gen_input to update input files to the latest format.
• Values in weight_soln may be different from that obtained in ver. 0.1.
• Changed random number generator to RANDOM_NUMBER() provided by Fortran compiler. Several values in reference system may be different from 0.1 because of this change (and changes in parallelization scheme).
• "corref" file is now output in binary format and is incompatible with old style format.
• Reference system computation now produces "progress.tt". The file contains the processed frame in the simulation.