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> >
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