GROMACS version: 2026.0
GROMACS modification: No
Hi everyone…I am trying to run a MD simulation on very large membrane protein complex that is basically embedded in a POPC bilayer. The system is solvated with water molecules and counterions as well. I am trying to run 5 replicate simulations, each of atleast 1000 ns. To speed-up my computation, I am trying to do a Hydrogen Mass Repartitioning. I am new to this and I am not sure what parameters do i tweak on my production mdp file. Looking at the resources that are available online, I could see that I have to do the following additions to my production.mdp file
mass-repartition-factor = 3
dt = 0.004 ; 4 fs
constraints = h-bonds
constraint-algorithm = lincs
lincs-order = 4
lincs-iter = 1
I am not sure if these are the best options. Can anyone who has implemented this in the past help me with this? Many thanks in advance.