Thank you for your reply.
On Sun, Nov 11, 2012 at 8:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/11/12 4:51 AM, rama david wrote: > >> Hi justin , >> >> Thank you a lot for your explaination. >> >> My opinion on the working of g_mindist -pi is that when it shows the >> distance between two atom >> of the protein is less than vdw cut off ( 1.4 nm ) , then protein see it >> periodic image, and it is the violation of pbc. >> Is these is right??? ( That is the shortest Periodic distance should be >> larger than vdw cut off 1.4 ) >> >> > This is correct, when considering a single molecule, i.e. it can't see > itself. If you have two proteins, and you choose the blanket "Protein" > group, you haven't determined anything, because now the calculation > involves multiple molecules. > > > If it is right, g_mindist say that The shortest periodic distance is >> 0.154938 (nm) at time 16162 (ps), >> between atoms 223 and 3270 >> This is less than 1.4 then Why it is not problem..??? >> >> > Because they're in separate molecules. Did you ever do as I suggested and > visualize this frame? It will be immediately apparent that there is no > problem. Please refer to textbooks or even simple Google searching for > explanations of the minimum image convention. As I said, it is described > in almost every reference text. > > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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