[gmx-users] Re: Test particle insertion extra coordinate

MPID mpmcgovern at wisc.edu
Mon Mar 5 00:54:52 CET 2012

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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