I want to do a QM/MM MD simulation for an enzyme with a metal ion. I tried just changing the “Options for QMMM calculations” section in the md parameter file (.mdp) of the equilibration step.
Changes made in the .mdp file are given bellow.
QMMM= yes
QMMM-grps= index group selected for QM level
QMmethod= PM3
QMscheme=normal
QMbasis=6-31G
QMcharge= charge of the selected QMMM-grp
QMmult= multiplicity of the selected QMMM-grp
Then tried the equilibration step with the command,
gmx grompp -c em01.pdb -f eq01.mdp -n index.ndx -p system.top -o eq01.tpr
But, this gives an error and a warning.
Error: Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.
Warning: The sum of the two largest charge group radii (16.311) is larger than rlist (1.000)
Please help me with this problem. What is SAsteps mean?
And I want to know about CP2K do we need to install it to do QM/MM MD simulations? If so, is there a difference in the gromacs commands?
It looks like you are using an old version of GROMACS. If you want to use CP2K, you should use the 2022 release. Then the charge group radii error will go away. And 2022 has no SAsteps option.
Yes. I am using GROMACS version 2018.1. Then should try with the latest version. Thank you.