New and improved features

Virtual site with single constructing atom

Added a virtual site that is constructed on top if its single constructing atom. This can be useful for free-energy calculations.

Density-guided simulations can apply matrix multiplication and shift vector to structures

The new mdp option “density-guided-simulation-shift-vector” defines a shift vector that shifts the density-guided simulation group before the density forces are evaluated. With a known shift vector that aligns structure and input density, this feature enables structure refinement to non-aligned densities without the need to manipulate the input density data or structure. The mdp option “density-guided-simulation-transformation-matrix” allows to define a matrix with which to multiply the structure coordinates, before the shift vector is applied. This allows arbitrary rotation, skewing and scaling of input structures with respect to the input densities. A typical use case are membrane-embedded proteins which cannot easily be shifted and rotated within membranes.

Lower energy drift due to SETTLE

GROMACS already applied an improvement to the center of mass calculation in SETTLE to reduce energy drift in single precision. Now the center of mass calculation is completely avoided, which significantly reduces the energy drift when large coordinate values are present. This allows for accurate simulations of systems with SETTLE up to 1000 nm in size (but note that constraining with LINCS and SHAKE still introduces significant drift, which limits the system size to 100 to 200 nm).

mdrun now reports energy drift

With conservative integrators, mdrun now reports the drift of the conserved energy quantity in the log file.

FEP using AWH

It is now possible to control the lambda state of a free energy perturbation simulation using the Accelerated Weight Histogram method. This can be used as one of multiple AWH dimensions, where the other(s) are coupled to pull coordinates.

Support for cyclic molecules in pdb2gmx

It is now possible to process cyclic molecules in pdb2gmx and generate GROMACS topology files for them.

Stochastic cell rescaling barostat

Implementation of the stochastic cell rescaling barostat. This is a first-order, stochastic barostat, that can be used both for equilibration and production.