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(NEW)
implemented reading of Gromacs .trr files (together with .gro files) with
trajectories; coordinates, velocities and forces can be read from these
files; PBC
cell parameters are now read from Gromacs .gro files; For
any trajectory, for example if it was read from a .xyz file, Chemcraft can
now compute velocities and forces by the differences between coordinates in
adjacent frames; “Structures
divider” tool has been implemented: if your molecule contains several
residues (bonded groups of atoms), Chemcraft can select the atoms in each of
them or in each group of residues with same molecular formula. This option
can be useful e.g. for crystallographers and for people working with
molecular dynamics, for example if you have a big system containing clusters
united by H-bonds, you can select all dimers, all trimmers, etc.; A
tool for analyzing the bonding information in your molecule is implemented:
for example, you can check how many H-bonds does your system have, including
H-bond with oxygen atoms attached to carbon atoms, etc.; Chemcraft
can now automatically compute the numbers of dimers, trimmers, etc. formed
by hydrogen bonds for each step in a trajectory; The
window “Tools/Chemcraft incorrectly identifies…” has been elaborated:
now it is slightly more intuitive and easy for understanding than in
previous versions, and some additional options have been added (in
particular, now by default the H-bonds are not identified for hydrogens
attached to atoms like carbons). The new features can be mostly useful for
molecular dynamics calculations, when the user needs to analyze the network
of H-bonds in his system (three new tools mentioned above); The
atoms can be now colored by their velocities or forces (previously atoms
were colored by their properties like Mulliken charges, now we have added
the properties in form of vectors to this tool); Bugfix:
in previous version the Fragments Extractor tool worked not sufficiently
properly for “+Spheres” button, which must show all atoms which are near
enough to current atoms (in previous versions, atoms in a cube were shown
instead of atoms in a sphere); Bugfix:
previous versions (no older versions) didn’t read the IR frequencies from
Orca4 output files; Fixed
a bug in latest versions of Chemcraft (not in earlier versions) – the
frequencies were not read from files in Molden format generated by Turbomole; Labels
on bonds can be shown (bond numbers, bond types); The
tools for computing effective size of the molecule or the molecule’s area
have been elaborated: now Chemcraft contains several tables of van-der-waals
radii used for these computations, with the possibility to choose a table,
and with citations for these tables. Previous versions of Chemcraft used the
table “Collisional radii”, and now it uses Van-Der-Waals radii by
Alvarez and Santiago (2013) by default, so the sizes of your molecules
computed via these utilities slightly differ with the ones computed by
previous versions (to get the same results, you can set the default table to
the 4th option “Collisional radii…”); Static
arrays have been replaced by dynamical ones, so now a molecule of any size
can be rendered, though maybe slowly (previously there was a limit of 80 000
atoms); The
code has been optimized for working with very big molecules, so now
Chemcraft can be used by molecular dynamics researchers dealing with systems
like 300 000 atoms; Some
elaborations with atoms selection tools, which can be helpful in some cases; Some
small elaborations.
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