[gmx-developers] Making CMAP not atomtype dependent

Marcelo Depólo marcelodepolo at gmail.com
Thu Jan 30 16:07:31 CET 2020


I've been investigating the implementation of CMAP in GROMACS and, as far
as I understood, the current CMAP format is based on atomtypes and not on
function numbers or based on atomnames, as GROMACS normally do.

Hence, if one develops two different CMAPs for two different residues (say,
ALA and LEU), it would lead to the same header for both (such as below),
which I believe would cause a crash.

[ cmaptypes ]
C N CT C N 1 24 24\

Considering that FFSB19 (
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00591) already uses
residue-specific CMAPs, would it be possible to either:

1 - implement the use of function numbers for CMAPs (that dummy '1' could
be used as a CMAP ID and called at the .rtp entry) or;

2 - make CMAP entry based on atomnames?

I am not expert in the GROMACS code so I would appreciate any inputs that
you may find relevant.

Thanks in advance.
Best regards,
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464
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