[gmx-users] Saving CPU time with constraints ?

[Ing. Vojtěch Spiwok]

Dear gromacs users/developers

I would like to run an MD of ligand bound in the binding site
of a protein with most atoms of the protein constrained (frozen).
Does GROwingMonstersAndCloningShrimps calculate an energy
for all atoms in every step even if they are constrained ? In other
words, does it worth to delete those atoms which are frozen and
too distant to site of interest to save CPU time ?
I appologise if this information is easy to find in manual or on
program site, I didn't succeed.

Thanks
Happy modelling

Vojtech Spiwok
Dept. of Biodhemistry and Microbiology
ICT Prague
Czech Republic