LD seed during steepest descent energy minimisation

User discussions
1

GROMACS version: 2023.4
GROMACS modification: No

A curious question came to mind when running a straightforward energy minimisation calculation using Steepest descent on a solvated protein bilayer complex. In the output of grompp I see:

Setting the LD random seed to 1845473272

Langevin Dynamics (LD), as the name suggests, is a dynamics integration of motion. I’ve checked the Gromacs documentation on “steepest,” and LD is nowhere mentioned.

What is this LD seed (not just a random seed, but a random LD seed) doing in the context of the steepest descent energy minimisation?

Thanks all :-)

Edit: as a partial answer to my own question I found this:
“ld-seed: (-1) [integer] used to initialize random generator for thermal noise for stochastic and Brownian dynamics. When [ld-seed] is set to -1, a pseudo random seed is used. When running BD or SD on multiple processors, each processor uses a seed equal to [ld-seed]”.

I use SD over multiple processors, and ld-seed is -1 by default. So, what component requires a random seed for a non-thermal SD calculation? There are no dynamics, so that rules out velocities.

3

I’m almost certain that the LD seed is printed and even set in the tpr, but is not used for steepest descent energy minimization.

4

Thank you, Magnus.

Sounds like LD is set regardless of the operation (e.g., steepest, cg, md…)

Thanks
Anthony