[gmx-users] CHARMM and FEP calculations

Wright, Louise Louise.Wright at warwick.ac.uk
Fri Aug 24 15:28:31 CEST 2012

I asked a similar question a year ago about implementing CMAP in FEP calculations for gromacs 4.5.4.  At the time I could not get the simulation to run with CMAP as it came up with:
Fatal error:
> Function type CMAP Dih. not implemented in ip_pert

Helpfully, Mark suggested a modification to the code to get round this issue, but I am unclear as to whether in the newer version of gromacs (4.5.5) CMAP terms can actually be scaled from state A to state B or whether for all values of lambda this part of the potential remains in state A even if I were to manually write state B CMAP terms in the topology file and the code no longer gives a warning.

In addition, for CHARMM, and other FFs, there are some dihedrals which have multiple potentials, using the dihedral function type 9.  I have manually specified the state B parameters for these (and all other dihedrals) in my topology file but get the error message:

  Cannot automatically perturb a torsion with multiple terms to different
  Please specify perturbed parameters manually for this torsion in your

Is there a way to implement scaling of these multiply defined dihedrals in FEP calculations?

Many thanks for your help


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