Looking for a way to speed up do_x3dna process.

[Karn4132]

Hello,

I'm a new user of do_x3dna and I've been trying to find the helical parameters of the damaged DNA - Protein complex.
I found the issue that sometimes - x3dna does not detect the damaged bp, so I tried adding -ref at the end of the command.|

do_x3dna -f ../new.xtc -s ../new.pdb -ref

Currently, this line of command seems to work perfectly.
However, by using the referrence structure for the calculation, it takes much longer than before to finish the process.

Is this a normal outcome for not using the base pair parameter of the trajectory?
It is worth to mention that my trajectory is pretty long and the old process actually took quite a while to finish. The new code made the calculation even longer than I expected.

Karn