In nvt.mdp file during protein-ligand complex MD Simulation, you have:
title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control
So, I guessed that 0.02 * 5000 = 100 ps and therefore changed the above values to this below:
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000 ; 20 * 5000 = 100 ps
dt = 0.02 ; 20 fs
; Output control
But on using the command,
gmx mdrun -deffnm nvt
I still get 50000 as number of steps for 100 ps.
HOW CAN I INFLUENCE THE NUMBER OF STEPS?
You should open your GROMACS folder and find the step5_production.mdp file. Open it in notepad and change the "nsteps" number.
It should be 0.5 million by default if you are using CHARMM GUI. Change it to whatever you like and save the mdp file. It should run the number of defined steps.
I hope I understood the question correctly.
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