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jrhaberstroh / cGromCorrFMO

Correlation computation package for gromacs
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Charged residues #1

Closed jrhaberstroh closed 10 years ago

jrhaberstroh commented 10 years ago

Topology files encounter "multiple entry" problems when reading a residue that is spontaneously protonated due to the pH. The current system allows only a single RES,ATM pair except in the case of BCX, meaning either all or none of the residues of a particular type will be protonated.

jrhaberstroh commented 10 years ago

Solved by changing the specification to [RES],[ATM][ID], and tracking the ID along each of the molecules of the system. Since the charges are initialized by finding matches in the lookup table using a binary search map, this x30 increase in entries is barely noticable.

Will not work if multiple proteins are present in the system, eg for an FMO trimer, because the protein timer does not reset. Not that any of this would work for anything but exactly this system.