Improvements to GROMACS tools¶
gmx grompp now checks dihedral coefficients sum¶
The sum of dihedral parameters of type 3 (i.e Ryckaert-Bellemans or Fourier dihedrals) is now checked during preprocessing. In free energy simulations, this sum must be equal in both states as it affects final results through dH/dl. Additionally, this sum should be zero when comparing potential energy values with other force field ports and simulation codes, but a non-zero sum does not otherwise affect the simulation (a simple note is emitted).
If gmx grompp rejects an interaction that was previously accepted,
then change the first coefficient to make the total zero. This leading
coefficient has no effect on the derivative of the energy (ie. the forces),
and thus no effect on the dynamics.
No parameters in default force fields in GROMACS were affected, so none have changed.
Added support for DSSP v.2 in gmx dssp¶
There is now the ability to choose between two different output modes: with polyproline helices search enabled (option “-polypro”, default and corresponds to the output of DSSP v.4) and with polyproline helices search disabled (option “-nopolypro”, corresponds to the output of DSSP v.2).
The number of averaging blocks for -evisco is now chosen by the user¶
The number of averaging blocks used when computing viscosity using Einstein formula was previously hard-coded to 4.
This number can now be chosen by the user via the -einstein_blocks flag of gmx energy.
When computing viscosity from very long trajectories, it may be preferable to have several averaging blocks
to obtain a more accurate average and avoid the long-time diffusive behavior of the pressure integral.
New features in gmx hbond¶
A set of additional functionality has been added: dynamic selections are now available (as well as detailed output for them in an atomic index file); added the ability to customize the geometric criterion for hydrogen bond formation using custom distances and angles (via “-hbr” and “-hba” flags respectively); added the ability to add any atomic elements as donors or acceptors of hydrogen bonds (via “-de” and “-ea” flags respectively).
Improve reading performance of large .gro files¶
gmx grompp is now up to 30% faster when reading system coordinates
from a large gro file.
Smaller sampling windows in gmx msd¶
Trajectories that save frames at higher than average frequencies can now be analyzed at more frequent sampling windows
using -trestart < 1.0 picosecond, down to 1 femtosecond.