It is the energy step size limit.

Not sure exactly what you mean by the second question but typically the number of iterations / steps for EM can be specified by number of force evaluations OR a tolerance on force gradient. Maximum number of iteration is given by : nsteps

Energy minimization perturbs the coordinates of individual atoms until the very high repulsive energies due to the way they are packed in the simulation box are eliminated or reduced.

Please read the online documentation : https://manual.gromacs.org/2021/reference-manual/algorithms/energy-minimization.html

If you read the theory of MD and the GROMACS documentation you will understand more.

Some tutorials on protein simulation are available as well : https://ringo.ams.stonybrook.edu/index.php/MD_Simulation:_Protein_in_Water

http://www.mdtutorials.com/gmx/lysozyme/05_EM.html

Thank you for your reply..

you are saying ..It is the energy step size limit.

emstep: (0.01) [nm]

Then how it is in unit of nano-meter ?.

Second thing is

I need to print the maximum number of iteration in shell script?. How can I do it?

Please help me out..

Ashok Kumar

It's in nanometers because that's the spacing you use to compute the new vector of positions, which then you use to compute the potential energy. You have two cuts, one is the emstep, which is putting a limit on the length of the trial steps, and the other is emtol, which is the real stop-point, that is when the force is smaller than this quantity (in kJ/(mol*nm)) then the algorithm stops.

Basically GROMACS is using emstep to start guessing a new position for your atoms, which will hopefully be at a lower potential energy. The new position is guessed by following the force, which is the negative of the potential energy gradient, therefore the systems is hopefully moving away from a high energy configuration (if you are using steepest descent). If that's the case (potential energy in new config is lower then in older config) then the trial position is accepted. The algorithm checks the values of the forces in the new point, if it's smaller than emtol then it stops (convergence reached) otherwise a new trial position is generated. In the other case, that is if the potential is higher than before, then the trial positions are rejected and a new one is generated from the previous step. Therefore GROMACS needs a starting guess for your steps, which is exactly what emstep is.

Read the documentation, the part of energy minimization under the chapter algorithms (pag 335-336 for steepest descent)

https://manual.gromacs.org/documentation/2021/manual-2021.pdf

This request is not clear:

I need to print the maximum number of iteration in shell script?. How can I do it?

What do you mean?