The following are a list of patches that fix bugs discovered after the NAMD 2.14 release.

• Fix constant-pH MD output. This patch fixes NAMD's statically linked compiled-in Psfgen implementation and its logging output.
  Download source code patch: namd_2.14_fix-constant-pH.patch
  Download pre-patched files: namd_2.14_fix-constant-pH.tar.gz


• Fix LJ correction for alchemical simulation. This patch fixes the LJ correction term ("LJCorrection on") calculation for alchemical simulation. Note that standard simulations have not been affected by this bug.
  Download source code patch: namd_2.14_fix-LJCorrection.patch
  Download pre-patched files: namd_2.14_fix-LJCorrection.tar.gz

To patch the source code for each of the aforementioned bugs, download the source release of NAMD 2.14, expand the archive file, change into the top level directory, and apply the patch. You can either download and apply a diff-generated patch, or you can download a tar ball containing the patched versions of the affected source files.

Here is an example of applying a diff-generated patch:

$ tar xvzf NAMD_2.14_Source.tar.gz
$ cd NAMD_2.14_Source
$ patch -p1 < namd_2.14_bug-fix.patch

Here is an example of updating from a tar ball:

$ tar xvzf NAMD_2.14_Source.tar.gz
$ cd NAMD_2.14_Source
$ tar xvzf namd_2.14_bug-fix.tar.gz

After patching the source code, you must rebuild NAMD from source.