GROMACS file support

NAMD has the ability to load GROMACS ASCII topology (.top) and coordinate (.gro) files, which allows you to run most GROMACS simulations in NAMD. All simulation output will still be in the traditional NAMD formats.

• gromacs $<$ use GROMACS format force field? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: If gromacs is set to on, then grotopfile must be defined, and structure and parameters should not be defined.
• grotopfile $<$ GROMACS format topology/parameter file $>$
  Acceptable Values: UNIX filename
  Description: This file contains complete topology and parameter information of the system.

• grocoorfile $<$ GROMACS format coordinate file $>$
  Acceptable Values: UNIX filename
  Description: This file contains the coordinates of all the atoms. Note that coordinates can also be used for PDB format coordinate file. When gromacs is set to on, either grocoorfile or coordinates must be defined, but not both.

However, NAMD does not have support for many GROMACS-specific options:

• Dummies (fake atoms with positions generated from the positions of real atoms) are not supported.
• The GROMACS pairs section, where explicit 1–4 parameters are given between pairs of atoms, is not supported, since NAMD calculates its 1–4 interactions exclusively by type.
• Similarly, exclusions are not supported. The biggest problem here is that GROMACS RB dihedrals are supposed to imply exclusions, but NAMD does not support this.
• Constraints, restraints, and settles are not implemented in NAMD.
• In some cases, it may not work to override some but not all of the parameters for a bond, atom, etc. In this case, NAMD will generate an error and stop. The parser will sometimes not tolerate correct GROMACS files or fail to detect errors in badly formatted files.
• NAMD does not support all the types of bond potentials that exist in GROMACS, but approximates them with harmonic or sinusoidal potentials.
• NAMD does not read periodic box lengths in the coordinate file. They must be explicitly specified in the NAMD configuration file.