@ Justin, Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character?
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 7:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/9/13 7:07 PM, Xu Dong Huang wrote: >> 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 >> > > The last line of the .gro file (box vectors) does not end in a newline > character. I discovered this by running: > > wc -l star.gro > > which returned 103, which would indicate that there should be 100 atoms in > addition to a title line, number of atoms, and box vectors. Since there are > 101 listed atoms, I knew there was a problem, likely with the last line. > Adding a newline character allows the structure to be opened in VMD. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- 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
