An X-PLOR PSF post-processor for alchemical free energy calculations in NAMD

Written by Jérôme Hénin


Version 1.4 (June 2009) - tiny fix to handle PSF-CMAP files properly.

As of NAMD 2.7b2, alchemify is not needed anymore, since all unwanted terms are discarded by NAMD at runtime. At this point, however, this does not apply to NAMD binaries compiled with the memory optimized option.


NAMD features an implementation of alchemical FEP that uses the dual topology approach. Dual topology requires that the initial and final groups do not interact. To prevent such interactions, the PSF file describing the system should:
Psfgen is not designed to handle nonbonded exclusion lists, and it is not straightforward to use it for removing unwanted bonded terms. Alchemify is a small program that takes care of these two tasks with minimal effort from the user.
For simulating single amino-acid mutations in proteins, the setup can be handled automatically by the VMD plugin Mutator.


alchemify <input PSF> <output PSF> <FEPfile> [FEP column]

How to use it



Alchemify is Free Software. It is distributed under the GNU General Public License, version 2.