Hello all. i tried to use charmm-gui in order to generate input files for simulation of my enzyme in water with gromacs . I have a gromacs subdirectory containing a gromacs inputs and a shell script template (in README) for running the inputs. there are three mdp files: step4.0_minimization.mdp, step4.0_minimization.mdp and step5_production.mdp.
but according to gromacs tutorials. we need nvt.mdp and npt.mdp.
Is step4.0_minimization.mdp for temprature equilibration? and we dont need pressure equilibration with charmm-gui?
Presumably you’ve got a typo here and there is a step4.1_equilibration.mdp or something similar.
There is no “one size fits all” for equilibrating simulation systems. The tutorial I wrote presents one possible method. It is not the only one.