Hi Kavya, > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps), > between atoms 2062 and 3688" > where 2062 is a protein atom and 21824 is a water molecule.
21824 is the time in ps at which the two atoms indicated, 2062 and 3688, are at the short distance given. You can dump the frame with trjconv and have a look. Probably your molecule stretched, or you solvated in a rectangular box and the protein rotated. In the first case, set a larger distance, in the second, use a rhombic dodecahedron. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
