request to speed up grompp

Hello,

(this is a feature request to speed up grompp dramatically).

I am trying to figure out why grompp is so slow when given a long lists of bonded interactions. For example, my base system takes 7 seconds to run grompp and 37 seconds to do 100 steps of EM. However, when I add ~250,000 distance restraints grompp takes 3 minutes, and when I add ~600,000 distance restraints grompp takes 18 minutes. In both cases, the mdrun command is almost as fast as it was without any distance restraints (~42 seconds in each case). I made a bit of progress by converting the distance restraints to type-6 bonds, in which case the addition of ~250,000 or ~600,000 type-6 bonds results in grompp finishing in 1.5 minutes and 6 minutes, respectively.

These numbers indicate to me that there is some type of non-linear slowdown when adding bonded interactions (like possibly a check for duplication of bonded terms as each one is read in, or memory reallocation).

I would appreciate it if anybody knows which routine I should look at to see if I can get rid of this grompp lag. I am currently working with gromacs 5.1.2. Newer versions should be OK, but since ideally I want to use energy group exclusions, gromacs-2020 and it's verlet-scheme-only code is probably not an option for me. However, I did verify that I get the same type of non-linear slowdown when adding many bonded terms to gromacs-2020.

• This was recently posted to the gmx users list: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-March/128882.html

Thank you, Chris.