Hello, Yes i did that. but qualitatively i did not see any such clashes. But i do not know how to quantify it by calculations.
Thank you with regards Kavya On Mon, Sep 26, 2011 at 5:51 PM, Sarath Chandra Dantu <dsar...@gwdg.de>wrote: > > > Hello again, > > > > I centered it and then did the calculation again for minimum image > > distance > > but still it showed the same graph as without centering. I tried > > visualising > > it > > using vmd but could not see any such clashes. since I am new to vmd > > I do not know whether it is possible to calculate such clashes if at all > > in vmd? I am using dodecahedron box. can it be visualised as it is in > vmd? > > > > In VMD go to graphics then representations and select periodic. In > periodic by clicking on +/- of each axis you can check if your protein > bumps into itself. > > Best, > > Sarath > > > Thank you > > With regards > > Kavya > > > > On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <hmkv...@gmail.com> wrote: > > > >> Thanks. > >> > >> > >> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <jalem...@vt.edu> > >> wrote: > >> > >>> > >>> > >>> Kavyashree M wrote: > >>> > >>>> Dear users, > >>>> > >>>> I was trying to simulate a protein dimer covalently bond with > >>>> a disulphide bond (230+230 aa long). I used usual protocol > >>>> as used for simulation of a monomeric protein, using gromacs- > >>>> 4.5.3, dodecahedron box, tip4p water model and protein to > >>>> box distance of 1 (-d in editconf). In the middle of the simulation > >>>> when i checked for minimum image violation there was huge > >>>> clashes. I am extremely sorry I have been asking regarding this > >>>> many times but in this it is a dimer and I am not sure what mistake > >>>> I have done because this happened while simulating another dimer > >>>> also though not sever. Hence I seek some guidance from this > >>>> community regarding the problem. I attach the graph herewith. > >>>> Kindly help. Let me know if I need to give any other information. > >>>> > >>>> > >>> Please see my post from yesterday for a more detailed reply to this > >>> exact > >>> same type of question. I am beginning to suspect there's a problem > >>> with > >>> g_mindist, but I have no solid evidence for that claim, just a hunch. > >>> It > >>> looks like your protein crosses a periodic boundary and that messes up > >>> the > >>> calculation. Please center the protein in the box with trjconv -center > >>> and > >>> re-analyze to see if there are any differences. > >>> > >>> -Justin > >>> > >>> -- > >>> ==============================**========== > >>> > >>> Justin A. Lemkul > >>> Ph.D. Candidate > >>> ICTAS Doctoral Scholar > >>> MILES-IGERT Trainee > >>> 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 > > > -------------------- > Sarath Chandra Dantu > Computational Biomolecular Chemistry > Max Planck Institute of Biophysical Chemistry > Am Fassberg 11, > Gottingen > 37077 > Germany > > Email: dsar...@gwdg.de > Tel: ++49-551-201-2320 > Fax: ++49-551-201-2302 > > > -- > 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 >
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