在运行命令gmx grompp -f pr.mdp -c em.gro -p topol.top -r em.gro -o pr.tpr后，出现note
NOTE 1 [file pr.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.
step 645: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
此前已进行多次能量极小化，使Fmax<100，还通过删除拓扑文件中[pairs]可能产生1,4 interaction的地方，消除了警告：
WARNING: Listed nonbonded interaction between particles 1836 and 1842
at distance 7.019 which is larger than the table limit 2.109 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.