Dear all, I created this .gro file following the gromacs format. But when I load it into VMD, it doesn't show the structure or molecule, and I have made many .gro before this one, and learned from many mistakes, but for this one, I don't know what I did wrong. I still proceeded to do simulation anyway and when I do energy minimization, I get an error of infinite normal force and etc (which I read past gmx list question that an atom is severely overlapping and causing the complication). Since I can't even view the .gro structure i made in VMD, I'm going to go ahead and assume there is something wrong with my initial structure to begin with, but I don't know where.
Here is the link to my .gro file + topology https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg Thanks for any input. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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
