Thanks a lot for the reply! I did as you said. I had a coordinate file where I wanted to add insert a water molecule withing a cavity. I added these lines to the .gro file: 340SOL OW 1274 2.925 0.061 2.677 0.2533 -0.1222 0.1294 340SOL HW1 1275 2.893 0.000 2.605 -0.1856 0.5697 -0.2686 340SOL HW2 1276 2.849 0.082 2.739 0.5491 -0.4502 0.6106 341INS X 2036 0.000 0.000 1.000 0.0000 0.0000 0.0000 I realize I still neeed to center the water molecule, but I am testing now. To make grompp work, I added a line in the .top file and called the last coordinate a CL- atom. I then can do grompp. But when I do mdrun -rerun, I get this error: Fatal error: Number of atoms in trajectory (2032) minus one is not equal the number in the run input file (2036) minus the number of atoms to insert (1) The math here seems to imply that the extra atom belongs in the trajectory rather than the tpr file, and also, it now thinks I'm inserting a CL- atom instead of water.
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