ERmod Code(deprecated)

138 lines (118 with data), 6.0 kB

version 0.4.alpha1 (24 Dec 2015)
* Real-space kernel was completely rewritten. Currrent version is very slow though.

version 0.3.5 (09/27/2016)
* Energy Histogram Computation:
    * gen_structure for NAMD now accepts NBFIX keyword
    * MODYLAS inputs are now supported in gen_structure and gen_input
    * User-defined meshes are accepted for energy coordinates
* Solvation Free Energy:
    * Dispersion correction on Lennard-Jones interaction in the slvfe
    calculation is calculted with a key of ljlrc, and the extensions/LJLRC
    directory is removed.
    * A script is prepared for assessing the convergence with respect to
    the reference-solvent run.

version 0.3.4 (12/24/2015)
* Energy Histogram Computation:
    * The ermod program terminates when the cell is not cuboidal
* Solvation Free Energy:
    * The number of logarithmic meshes is internally counted in slvfe

version 0.3.3 (10/22/2015)
* Bug fixes:
    * Fixed a bug in non-cuboidal box. (update: this was not enough.)

version 0.3.2 (09/26/2015)
* Energy Histogram Computation:
    * CHARMM and LAMMPS inputs are now supported in gen_structure and gen_input (undocumented at the moment)
    * PPPM computation is implemented
    * Gromacs-type force switching is implemented
    * Micelle, lipid membrane, and protein can consist of more than a single
    species

version 0.3.1 (06/08/2015)
* Bug fixes:
    Fixed GROMAS gen_structure cannot specify solutes in interactive way

version 0.3.0 (06/01/2015)
* Bug fixes:
    GROMACS topology file parsing is now case sensitive
    (it was case insensitive to match pre-4.0 behaviour, which is now outdated)

version 0.3.rc1 (05/07/2015)
* Energy Histogram Computation:
    * The extension of energy representation with intermediate states is implemented (experimental). 
* Solvation Free Energy:
    * The numbers of soln/engsln.XX and refs/engref.XX files are counted
    internally within the slvfe program.
* Error reporting:
    * NBFIX keyword in PSF files, which was not correctly handled, is now reported as an error.
    * When input atoms are not contiguous, gen_structure generates error instead of warning. Users
    can fall back to the old behaviour by reverting changes manually.
* Bug fixes:
    * mpi_info conflicting with MPI-3.0 is now removed
    * Blacklisted ifort 12.1.x which emits broken codes.
    * Misc. configure bug for compiling option

version 0.3.beta1 (02/08/2014)
* Energy Histogram Computation:
    * Non-orthogonal periodic box is now correctly handled.
    * Treatment of asymmetric slab geometry is made possible.
* File I/O:
    * Added ERMOD_FORCE_PLUGIN_TYPE environment to coerce file format detection.
* Bug fixes:
    * A workaround was implemented in configure agaist a bug in MKL ver 10.3.
    * Workaround cpp's error when using AMBER force field in GROMACS. This is not perfect (yet).
    * Some histogram parameters are no longer adjustable (ticket #7)

version 0.3.alpha8 (04/10/2013)
* Solvation Free Energy:
    * Added dispersion correction on Lennard-Jones interaction in the modified
    slvfe.F90 program prepared in the extensions directory. THIS WILL NOT
    BE ENABLED BY DEFAULT! See extensions/README_LJLRC for details.

version 0.3.alpha7 (04/08/2013)
* Energy Histogram Computation:
    * The gromacs-type potential switch and the force switch for the LJ
    interaction are implemented with a new key of ljswitch.
* Misc:
    * A key of insstructure is introduced to select some solute structures
    according to the solute RMSD relative to the reference structure.
    * A procedure is defined which conducts a best-fit of
    the host (presumably protein) to the reference structure
    and inserts the solute (presumably ligand) within an given range of RMSD.

version 0.3.alpha6 (02/21/2013)
* Misc:
    * A snapshot can have its own weight; the weight information is saved in a
    separate file. The name of the file storing the weight is SysWght for the
    solution and for the solvent, and is SltWght for the isolated solute used
    for test-particle insertion. To activate the weight input, wgtsys = 1 in
    the case of SysWght and wgtins = 1 in the case of SltWght in
    parameters_er.

version 0.2.4 (02/13/2013)
* Misc:
    * There was a bug in case that the soln system contains more than one
    molecules for the solute species, and this bug is fixed
    * When the ermod program is used with an NAMD trajectory, it is no more
    necessary to prepare a .xst file. The cell information is directly read
    from the .dcd file and the file of HISTCELL linked to .xst file is not
    created by the gen_input script.

version 0.3.alpha5 (01/30/2013)
* Misc:
    * The ermod program does not output the self-energy distribution slfeng.XX
    at default. A key of selfcal is defined to output the self-energy
    distribution.
    * There was a bug in case that the soln system contains more than one
    molecules for the solute species, and this bug is fixed
    * When the ermod program is used with an NAMD trajectory, it is no more
    necessary to prepare a .xst file. The cell information is directly read
    from the .dcd file and the file of HISTCELL linked to .xst file is not
    created by the gen_input script.
    * The predetermined directories and filenames for the slvfe program is now
    flexible.

version 0.3.alpha4 (05/06/2012)
* Misc:
    * trajectory-formats/modylas.F90: Added I/O for Modylas MD package
    * mol_dissect: Fixed bugs with "save" command, reads PermIndex (so it now supports AMBER output), reads/writes sltpick

version 0.3.alpha3 (04/12/2012)
* Misc:
    * tools/AMBER/gen_input: --flexible is now abbreviated to -s.

version 0.3.alpha2 (03/19/2012)
* Parameters:
    * The specification for insertion configuration is rewritten with much more general setting.

version 0.2.3 (03/19/2012)
* General:
    * ERMOD is now licensed under GPL v2 or later.
* Install:
    * Fixed compilation problems on FX10 from Fujitsu.