Next: Creating PSF Structure Files
Up: Input and Output Files
Previous: AMBER file and force
Contents
Index
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.
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.
Next: Creating PSF Structure Files
Up: Input and Output Files
Previous: AMBER file and force
Contents
Index
http://www.ks.uiuc.edu/Research/namd/