Thank you justin, I actually check these file in vmd by seeing its periodic image , but I not seen any problem in PBC.
As per you, If protein contain multiple chain, I have to make the index group for each one. Then I have to check each one by g_mindist -pi Is these right??? But what wiil be the problem if I used the whole group???? Still I not get the your explanation..Pardon me, but please explain it again?? On Sat, Nov 10, 2012 at 8:34 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/10/12 10:02 AM, rama david wrote: > >> Dear justin, >> >> Thank you for your reply and explanation, >> >> My ligand is protein( 4 amino acid peptide). >> The group in index file PROTEIN contain both ligand >> and protein. >> >> The box size is 11.4942 10.7884 10.7884 at the time 16162 (ps). >> >> The box size I given in editconf is 11.40000 10.70000 10.70000 >> >> So please would you told me the reason for my g_mindist value less than >> vdw >> cut off 1.4 ????? >> >> > Look at what those atoms are at that particular time point. The confusion > likely arises from the fact that you're selecting "Protein," which actually > contains multiple molecules, rather than a single protein molecule. Atoms > can come pretty close during a simulation, especially if they are involved > in, for instance, hydrogen bonds. > > > -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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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
