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?
Thank you With regards Kavya On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <[email protected]> wrote: > Thanks. > > > On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <[email protected]> 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 [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> >> > >
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