LATEST FEATURES AND BUG FIXES:

 

** VERSION 3.3.0 **

(11 January 2024)

  • New sub-menu for the analysis of computed data from the main module (e.g., outputted frames). This includes the possibility to find dimeric molecular units and the computation of their interaction energy. The output is a PDB file with the dimers and corresponding energy contributions (Coulomb and VDW), and a file with data to plot the energy variation as a function of the distance between the centers of mass of the molecules.
  • Solved a problem related to the compilation of the libxdrf library, due to a support change in the more recent OSs (e.g., Debian-based operating systems).

  • ADITIONAL NOTES:

     - In the Users manual, page 3, where it reads:

                    "sudo .pre-install.sh"

      should be

                    "sudo ./pre-install.sh"

    - After compiling the program confirm that the folder "/usr/local/lib" is included in the LD_LIBRARY_PATH. To check this, run " echo $LD_LIBRARY_PATH" in your terminal. If not, include this path.

 

** VERSION 3.2.0 **

(22 January 2021)

  • A new aggregation type of calculation, which is based on a type 2 procedure, is now available. In this case, after the initial analyses, it allows to exclude molecules depending on their number of neighbors.
  • Center large molecules (e.g., polymer chains) at the center of the simulation box (see more).
  • Computation of aggregates apparent volume using a variable number of vectors and for a single molecule
  • New advanced menu section, which allows: (i) control reconstruction of broken molecules; (ii) trajectory read control; (iii) apparent volume calculation options
  • Improved output report, which includes glitch corrections and printing additional information about the calculation and system topology.

Bug Fixes

  • Memory leak problem solved.
  • Improved compatibility with GROMACS topology files
  • Corrected problems during ETA calculation

 

** VERSION 3.1.6 **

(21 August 2019)

    CAUTION: a memory leak occurs when the first shell analysis is performed. The origin of this problem is under investigation. Apparently, it only happens when the program was compiled using GFORTRAN 7.0 or higher. The program memory usage was improved to minimize this issue, but a permanent fix is expected to be released only in the near future.

Bug Fixes

  • Corrected problem while handling periodic boundary conditions with trajectories of triclinic simulation boxes produced with LAMMPS.

 

** VERSION 3.1.5 **

(9 August 2018)

New Features

  • Compatibility improvement with GROMACS *top files.
  • SDFs are now computed with units in nm-3 and normalized considering a uniform particle density when type 5 calculation is used
  • Other small tweaks!

Bug Fixes

  • Corrected the problem that prevented the calculation of CDFs with normalization.
  • Corrected problem when reading *PDB files in a folder.

 

** VERSION 3.1.4 **

(8 March 2018)

New Features

  • It is now possible to compute the bonds, angles and dihedrals for each molecule in the simulation box, for each step.
  • Extended support for LAMMPS trajectory files.

Bug Fixes

  • Fixed issue that could prevent the program to read from GROMACS topology files.
  • Fixed issue that could lead to a wrong assignment of molecules during molecular conformation analysis.

 

** VERSION 3.1.3 **

(19 September 2017)

New Features

  • New user interface.

Bug Fixes

  • Corrected problem reading Gromacs topology files.
  • Corrected memory allocation problem using calculation options 3 and 4.

 

** VERSION 3.1.2 **

(28 July 2017)

New Features

  • Allows to restrain 1st shell calculation according to VDW radii.
  • Perform 1st shell analysis between different molecules.
  • Revision of the normalization procedure of CDFs.
  • Ability to write conformational CDFs as matrices.

Bug Fixes

  • Corrected problem related with the computation of conformational combined distribution functions.

 

** VERSION 3.1.1 **

(17 February 2017)

New Features

  • It is now possible to read multiple trajectory files.
  • A few tweaks of the code and at questionnaire.

Bug Fixes

  • Solved issue related with the setup of the packing coefficient calculation.
  • Fixed atoms identification problem while using PSF files and when the program is compiled with Intel® Fortran Compiler.
  • Solved issue that prevents the correct reading of LAMMPS trajectory files.

 

** VERSION 3.1 **

(17 January 2017)

New Features

  • Computation of combined conformational analysis (CCA).
  • Restrain the computation of CDFs, SDFs, FSAs, CAs and CCA according to the number of neighbors of the molecules in the aggregates.
  • Record a PDB trajectory file with the molecules that compose the aggregates.
  • Other small tweaks and optimizations.
  • Ability to read GROMACS topology files.

Bug Fixes

  • Corrected bug while performing the simultaneous calculation of several conformational analysis.
  • Corrected bug while reading PSF files, when the program was compiled with Intel® Fortran Compiler.

 

** VERSION 3.0 **

(01 September 2016)

New Features

  • Ability to read trajectory files from GROMACS and LAMMPS, and also to use PDB files.
  • Computation of CDFs, SDFs, FSA, and molecular conformational analysis.
  • Ability of restrict the configurations used in the analysis.
  • The questioner was redesigned, and new features implemented to avoid problems in the calculations.
  • Calculation of the average number of aggregates during the simulation and distribution of the number of neighbors.
  • Record of the Aggregates in the simulation box in PDB files, colored according to the number of neighbors of the molecules.
  • Several other tweaks and optimizations.

 

** VERSION 2.3.1 **

(11 December 2015)

New Features

  • The connectivity criteria can now be based in the Van der Waals radii, Rvdw, of the atoms involved in the evaluation. Giving atoms A and B the criteria, D, is defined as: D = Rvdw(A) + Rvdw(B) + Cte, where Cte is a constant value, that can be defined by the user. The atoms names are automatically retrieved from the initial two letters of the atoms name and, the following atomic species are recognized: H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Se, Br, Kr, I and Xe. For an unidentified item a value of 1.75A is assumed. The program is case sensitive. Thus "CA" and "Ca" can be used in the same run to define an aromatic carbon or calcium atom, respectively.
  • For the aggregate volume calculation using VdW radii, a constant value can also be added as described above.
  • In this version all calculation reports are recorded in different files, avoiding overwriting previous results. For this purpose, an incremental index is added to the output files that now take the form AGGOUT_xxx.dat. The output files also contain a description of the calculation details.
  • The program is now able to record an input file (INPUT_xx) that can be used to run the program with the same conditions in a future calculation or for sequential calculations.

 

** VERSION 2.3 **

(24 August 2015)

New Features

  • Ability to read CHARMM output files (*.dcd and *.psf);
  • Calculation of aggregates area and volume using atomic VDW radii. The new option relies in the GEPOLE (J. Comput. Chem. 1991, 12, 1077-1088) and ARVO (Comput. Phys. Comm. 2005, 165, 59–96) codes and, by default, uses Van der Waals radii recommended by Bondi (J. Phys. Chem. 1964, 68, 441-451; Chem. Eng. News. 2009, 87, 19);
  • Analysis of aggregates composed by different centers (in the same or different molecules). For example, between OH groups in different molecules, that form continuous chains of hydrogen bonds (alternance between the centers is not required, as in the case of the polar networks of ionic liquids).

Bug Fixes

  • Major memory optimization to handle large simulation boxes and trajectory files;
  • Problem regarding the computation of average number of neighbors in large simulations.