I generated a solution using Solution Builder from CHARMM-GUI and
the equilibration step setup was as below:
gmx grompp -f /equi_prefix}.mdp -o{equi_prefix}.tpr -c {mini_prefix}.gro -r {init}.gro -p topol.top -n index.ndx
the ${init}.gro file is a structure before minimization step. Additionally, protein and dihedral were restraint by defining DPOSRES and DHIDRES in the mdp files.
Is it necessary to restrain initial structure before minimization during equilibration?
The reason to restrain some things during initial EM or MD is to resolve strong forces by moving things that either (a) you have less information about or (b) have shorter conformational autocorrelation times. Usually both. So if an auto-added water molecule is too close to your protein, then you want the water to move, not the amino acid. Once everything is more within the bounds of likely configurations, you can release these artificial restraints.
thank you very much for your reply. Suppose the position restrain enhance the performance? I compared equilibration step with and without the position restraints and its giving almost the same performance. Where can I see if the position restraints are working correctly?