Tuning the gen_seed value for replicate simulation

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No

Hi community members,

I have been simulating a protein-ligand complex in POPC bilayer. I have completed a 150 ns simulation run and now would like to set up a couple of replicate simulations just to make sure that my replicate simulations have a different starting microscopic states with different velocities etc. I have read the literature and found out that I have to tweak the value of gen_seed in mdp file. Do I need to do this tweaking in NVT.mdp, NPT.mdp and MD.mdp files or is there a correct way to do that. Unfortunately I have no idea how should I proceed with that. Can some one help me with this. I will be really grateful.

Many thanks in advance

Best regards

2

Hi,

So I got some reading done regarding this. What I have figured out is changing the
following velocity generation parameters in the NVT.mdp file will be sufficient to change the velocities:
gen_vel = yes ; assign velocities from Maxwell distribution
gen_seed = -1 ; generate a random seed

So I will have to run 3 separate simulations of 150 ns and each one will have a the gen_vel = yes and gen_seed = -1 for generating random velocities of the system. This will only be effective in NVT.mdp file. I will not be making any changes in NPT.mdp and md.mdp files since regenerating velocities at each step might negate the purpose of previous equilibration.

Is this the best approach to run 3 replicate simulations for my system of interest? Can come one share their insights on this topic?

Best regards

3

Yes, velocities are only ever generated once - whatever you run immediately after energy minimization (because the atoms in the system have no velocities at that point).