Dear gromacs users,
I am running a protein-ligand umbrella sampling simulation using protein-ligand distance as the reaction coordinate. I have obtained the conformations necessary for 50 umbrella windows from steered MD simulation and now running umbrella sampling MD starting with the 50 initial conformations.
I modifed the unbiased production MD mdp file and added the pull-code setting for umbrella sampling. Now for the unbiased production mdp file, it contains “continuation = yes” as I have been using the: “grompp -t state.cpt -c out.gro” for running successive equilibration simulations. But for the umbrella sampling there is no need to use a checkpoint file, I used simply: “grompp -f umbrella1.mdp -c window1.gro -p topol.top -o run.tpr”, without using the -t flag. However, unknowingly the “continuation = yes” option is kept in the mdp file.
Now my question is that if we are not using the -t flag to include cpt file during grompp step, does this continuation = yes affect the umbrella sampling simulation in any way? Even if it does, is the effect going to be significant or it does not really matter during umbrella sampling simulations? Any help would be much appreciated, thank you.