Improvements to GROMACS tools#

Improved Einstein viscosity calculation in gmx energy#

Viscosity calculation using the Einstein formula is convenient as this does not require extremely frequent pressure tensor data. However, the implementation of the calculation was inconvenient for long simulations and could take hours to complete. Improved stepping through the data reduces the computational time to minutes and provides much clearer output.

XVG output from gmx rdf now uses 6 decimal places#

The output from gmx rdf now uses more decimal places in order to avoid rounding issues. These issues led to perceived erroneous shifts in the results.

Issue 4647

Handle CYX-CYX disulfide bonds in gmx pdb2gmx#

Naming CYS residues as CYX shows that they should form a disulfide bond. gmx pdb2gmx will now correctly interpret them as disulfide bond forming residues.

Issue 4929