NAMD Wiki: Namd27b1Release

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Issues with the 2.7b1 release of NAMD.

When minimizing a system with bad contacts involving fixed atoms, the minimizer will incorrectly move fixed atoms during the initial "slowly moving atoms with bad contacts downhill" startup process. Fixed in CVS.

For those using the CHARMM31 parameters from please note:

  • Most patches now require the use of "regenerate angles dihedrals" (in psfgen) after they are applied. Older versions included the angle and dihedral corrections in the patch. However, when psfgen regenerates angles it will ignore the "auto none" specification for water segments, and hence any water with a "third bond" between the hydrogens will have extra angles generated. The solution is to remove the third bond from the topology file.
  • The HSP residue is missing a CMAP term. It can be easily copied from, e.g., HSD.

Warning: 1 processors are overloaded due to high background load.

Mostly harmless. Please see the discussion in NamdWarnings.

Please see the release notes at