On 24/08/2012 11:28 PM, Wright, Louise wrote:
Hi
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.
I expect the latter, since
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x makes
no mention of CMAP and FEP. Someone would have to want to do the coding
and testing work to make this possible.
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
form.
Please specify perturbed parameters manually for this torsion in your
topology!
This error pertains to what grompp can look up in ffbonded.itp for this
interaction, and is perhaps over-zealous, but without seeing the
relevant file fragments it's hard to say anything.
Mark
Is there a way to implement scaling of these multiply defined dihedrals in FEP
calculations?
Many thanks for your help
Louise
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