Secondary Structure

Secondary Structure collective variables (ALPHARMSD, PARABETARMSD and ANTIBETARMSD) can be particularly demanding if you want to calculate them for all the residues of a protein. This is particularly true for the calculation of beta structures.

The FIRST thing to speed up PARABETARMSD and ANTIBETARMSD is to use the keyword STRANDS_CUTOFF (i.e. STRANDS_CUTOFF=1), in this way only a subset of possible fragments, the one less than 1.0 nm apart, are used in the calculation.

The metric used to calculate the distance from ideal secondary structure elements can also influence the performances, try to use TYPE=OPTIMAL or TYPE=OPTIMAL-FAST instead of TYPE=DRMSD.

At last, try to reduce the number of residues in the calculation.