Changes from previous versions

The changes made from 5.2.0 to 5.3.0

v 5.3.1 Rg utility in the tranal suite to compute gyrationradius and end-to-end distance
Tranal utility accept .itp files in Gromacs format describing individual molecules
v. 5.3.0 A new version of the expanded ensemble mode implementing L2MC algorithm: A.Nikitin, V.Milchevskaya, A.P.Lyubartsev "To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC", J. Comput. Chem., 42, 787 (2021)
Additional combination rule for Lennard-Jones interations from paper: A. Nikitin, Y. Milchevskiy, A. P. Lyubartsev "AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes" J. Phys. Chem. B, 119, 14563-14573 (2015) DOI: 10.1021/acs.jpcb.5b07233
v. 5.2.8:
The main input file name should be given as an argument to the “md” or “mdp” executable both in serial and parallel execution
Flexible SPC water model accept internal bond parameters from the .mmol file
Control of large temperature deviations became optional
v. 5.2.7: The pair list describing special Lennard-Jones interactions (owerwriting combination rules) can be automatically generated from the force field file (.ff) and atom types present in the molecular description files (.mmol).
Extentions to the force field file format are added
Support for TRIPOS .mol2 file format (as produced by Avogadro molecular editor and the antechamber package) in the makemol utility is added.
Changed interface to the makemol utility
v. 5.2.6: Module cifo, converting crystallografic information in .cif format to MDynaMix .mmol and .smol molecular description formats, is added (contribution by Dmitrij Lioubartsev).
Option for special Lennard-Jones parameters for 1-4 neighbours in a molecule is introduced (parameter par14 in .mmol file). Makemol utility is updated to use this option.
Special Lennard-Jones interactions between any atom pairs (different from the parameters of .mmol file and what is determined by the combination rules) can be also introduced using “pair list” option of the input file.
Option for on-the-flight computation of radial distribution functions is depriciated
v. 5.2.5: Soft core potentials are implemented in computations of solvation free energies by the expanded ensemble method, see: J.M.P.Jämbeck,F.Mocci, A.P.Lyubartsev, A.Laaksonen, "Partial atomic charges and their impact on the free energy of solvation". Journal of Computational Chemistry, 34, 187-197 (2013), Supporting Information.
Option for “gravitation”-like force acting along Z-axis on molecules of a certain type is added
Option for on-the-flight computation of time correlation functions is depriciated
v.5.2.4: Algorithm for WL iterations is changed. One WL interations is no longer linked to parameter Serie_average , but is determined by requirement that the system has walked at least Num_pass (default 2) times between the end subensembles.
Module restime.f , computing residense times, is added to the analysis suite.
.mmol file are no longer necessary for some types of analysis of trajectories.
v.5.2.3: A bug corrected which lead to incorrect computations of solvation free energies for large molecules due to incorrect computations of intramolecular nonbonded electrostatic interaction (affect versions 5.2.1-5.2.2)
v.5.2.2: In the expanded ensemble mode, an automatic tuning of balancing factors using Wang-Landau algorithm is implemented (contribution by Nikolai Volkov)
v.5.2.1: Option for semianizotropic NPT ensemble, with separate pressure control along Z-axis and in XY-plane, is introduced

The changes made from v.5.1 to 5.2:

Expanded ensemble method for calculation of solvation free energy is now included into main MDynaMix package. The program computes the free energy difference upon addition of one or several molecules. Automatic tuning of balancing factors using Wang-Landau algorithm is implemented
Option for “semiisotropical” NPT ensemble with separate pressure conrol in Z direction and in XY plane is introduced
Option for gradual change of volume (density) to a target value