How to define independednt initial condition for simulation in Gromacs (gen_seed or ld_seed)?

User discussions
1

Dear Gromacs users,

I would like to perform 5 independent simulations (different initial conditions) of water diffusion in zeolite to study the effect of initial conditions on the diffusion coefficient of water.
I discovered that the .mdp file has the gen_seed and ld_seed options. However, I could not correctly understand the difference between these options. Also, I don’t know how to define numbers for independent simulations. 1,2, … or other numbers?
Could you please explain the differences? Also, what numbers can be used for that?

Best

2

gen-seed is the seed to generate random initial velocities (with gen-vel = yes).

ld-seed is used to control the temperature during the simulation, if you use sd or bd integrators or with the v-rescale thermostat.

3

Dear Magnusl,

Thanks for your reply.

Then I need the gen_seed option. How can I define other numbers except(-1)? Is there any specific rule for that?

4

It is a random seed (Random seed - Wikipedia). You can set it to whatever integer you want. Unless you want to generate the same velocities, e.g., to reproduce (in theory) a previous simulation, there is no reason to set it to anything else than the default -1, giving a (semi-)random seed.

5

Thanks a lot for your descriptions.

Best