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 ????? With best wishes and regards, Rama david On Sat, Nov 10, 2012 at 7:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/10/12 8:44 AM, rama david wrote: > >> Hi justin , >> Thank you for reply. >> Mdp parameters are as follow , >> >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> rlist = 0.9 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) >> vdw-type = Cut-off >> rvdw = 1.4 ; short-range van der Waals cutoff (in nm) >> >> I choose the protein for g_mindist option.. >> >> Please could you explain me what am getting and why it is not violation of >> pbc???? >> >> > Before you said you had a protein and ligand. Is the ligand itself > actually a protein? > > PBC artifacts arise when you violate the minimum image convention, that > is, the same interaction is calculated multiple times, thus leading to > erroneous contributions to the forces and flawed dynamics. If you avoid > double-counting of interactions by setting an appropriately sized box, > these don't occur. > > The only way I would see any spurious interactions occurring in your case > is if the box massively shrank (which probably would have caused the system > to crash anyway) or if any protein molecules unfolded. Stable, well-folded > proteins placed in suitably sized boxes generally do not experience PBC > artifacts, and the evidence you have presented thus far is not indicative > of any problem. > > > -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
