Hello sir, I had used a dodecahedron cell for simulation. I have run the simulation for 100ns, did you man I have to restart the simulation again?
Thanking you Kavya On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <[email protected]> wrote: > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
