The error is correct. After inspecting the code, the extra coordinate (coordinate of the cavity) is taken from the last atom of the trajectory (rerun_fr.x) and not from the .tpr file (mdatoms). This is weird, but allows different cavities for different frames I guess...
I am guessing you can add the extra coordinate (cavity coordinate) to each frame. You just need to convert from a binary version (.xtc, .trr) to a ascii version (.gro, .g96), add the coordinate, convert back to binary (optional, but saves space), and make the rerun over this. Be _careful_ with the conversions not to screw the original trajectory. Plus, with this, there is no need for topology mambo-jambos (calling CL- to the cavity location, etc). I did not remember this because I hacked the code and I bypass that part, giving the extra coordinate (cavity) through a variable. I hope this solves your problem. Best, João On Sun, Mar 4, 2012 at 11:54 PM, MPID <mpmcgov...@wisc.edu> wrote: > 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. > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546192.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613
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