In the develop python3-adapted branch, I am a bit puzzled with the logics behind this line
To give an example, if I try to modify *-C into *-CC, hydrogens of methyl group are never mapped to hydrogens of the first carbon of ethyl group. Thus, efficiently in the resulting hydrid topology carbon will be bonded to 5 hydroges (three real ones and two dummy ones). This actually blocks using the hmr with GROMACS. But it also looks a bit strange to me in general.
@vgapsys Could you maybe share the idea behind this line? I tested internally and with commenting out this condition I am getting reasonable mappings which I can use with hmr. The following code maps hydrogens to minimize rmsd, which makes sense to me and allows runs with hmr.
In the
developpython3-adapted branch, I am a bit puzzled with the logics behind this lineTo give an example, if I try to modify *-C into *-CC, hydrogens of methyl group are never mapped to hydrogens of the first carbon of ethyl group. Thus, efficiently in the resulting hydrid topology carbon will be bonded to 5 hydroges (three real ones and two dummy ones). This actually blocks using the hmr with GROMACS. But it also looks a bit strange to me in general.
@vgapsys Could you maybe share the idea behind this line? I tested internally and with commenting out this condition I am getting reasonable mappings which I can use with hmr. The following code maps hydrogens to minimize rmsd, which makes sense to me and allows runs with hmr.